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Bacterial transcription

Bacterial transcription is the process by which a single multisubunit RNA polymerase (RNAP) enzyme synthesizes RNA molecules from a DNA template in the cytoplasm, serving as the primary mechanism for gene expression in bacteria.^[1] This process produces messenger RNA (mRNA) for translation into proteins, as well as functional RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA), and is tightly coupled with translation due to the prokaryotic organization lacking a nuclear membrane.^[2] In model organisms like Escherichia coli, transcription is divided into three main stages: initiation, where RNAP recognizes and binds promoters; elongation, where RNA is synthesized processively; and termination, where RNAP dissociates from the DNA and releases the transcript.^[3] The process is highly regulated to control gene expression in response to environmental cues, with promoter strength varying from less than one to tens of thousands of RNA copies per cell generation.^[1] Recent cryo-electron microscopy (cryo-EM) studies as of 2024 have provided high-resolution insights into RNAP dynamics during initiation and elongation.^[4] The bacterial RNAP holoenzyme, formed by the core enzyme (subunits α₂ββ'ω) and a dissociable sigma (σ) factor, is central to transcription and conserved across bacterial species.^[3]

The Transcription Machinery

RNA Polymerase Structure

The bacterial RNA polymerase (RNAP) core enzyme, responsible for catalyzing RNA synthesis, consists of five subunits: two α subunits (α₂), one β subunit, one β' subunit, and one small ω subunit.^[5] The α subunits, each approximately 36 kDa, primarily facilitate the assembly of the core enzyme and mediate interactions with regulatory factors.^[5] The β subunit (~150 kDa) contributes to the formation of the catalytic site and binds the nucleotide substrate, while the β' subunit (~155 kDa) forms the channel accommodating the DNA-RNA hybrid and houses key elements of the active site.^[5] The ω subunit (~10 kDa) stabilizes the core complex and aids in β' folding.^[5] Together, these subunits assemble into a ~400 kDa multi-subunit enzyme capable of processive RNA polymerization.^[6] The overall architecture of the bacterial RNAP core enzyme resembles a crab-claw shape, with the β and β' subunits forming the pincer-like lobes that create a central cleft for DNA binding and RNA synthesis.^[5] A prominent structural feature is the clamp domain, primarily within the β' subunit, which undergoes conformational changes to grip the downstream DNA duplex and maintain enzyme processivity.^[7] At the active site, located deep within the cleft, two Mg²⁺ ions are coordinated by three conserved aspartate residues (Asp460, Asp462, and Asp464) from the β' subunit of Escherichia coli RNAP to facilitate nucleotide addition via the two-metal-ion mechanism.^[8] This mechanism positions the 3'-OH of the growing RNA chain and the α-phosphate of the incoming nucleoside triphosphate (NTP) for nucleophilic attack, forming a phosphodiester bond and releasing pyrophosphate (PPi).^[8] The phosphodiester bond formation reaction is depicted as:

(\text{RNA})_n + \text{NTP} \rightarrow (\text{RNA})_{n+1} + \text{PP}_\text{i}

This reaction, powered by the hydrolysis of the high-energy phosphoanhydride bond in NTP, is conserved in all multisubunit RNAPs and relies on the precise positioning of the two Mg²⁺ ions to stabilize the transition state.^[8] The core enzyme structure exhibits high evolutionary conservation across bacterial phyla, reflecting its essential role in transcription, with the β and β' subunits showing the greatest sequence and structural similarity.^[9] However, subtle variations exist; for instance, Firmicutes such as Bacillus subtilis have slightly larger β' subunits and differences in the clamp region compared to Proteobacteria like E. coli, potentially influencing accessory protein interactions.^[9] Key insights into the RNAP structure have emerged from X-ray crystallography and cryo-electron microscopy (cryo-EM) studies since the 2010s, building on earlier lower-resolution models.^[5] A landmark 2.76 Å cryo-EM structure of the E. coli RNAP holoenzyme in complex with promoter DNA, published in 2015, revealed atomic details of the active site channel and clamp dynamics, confirming the crab-claw architecture and Mg²⁺ coordination.^[10] These high-resolution structures have illuminated how the core enzyme accommodates the DNA-RNA hybrid (8-9 base pairs) within a narrow cleft (~25 Å wide).^[10]

Sigma Factors and Promoters

Sigma factors are dissociable subunits of bacterial RNA polymerase holoenzyme that provide specificity for promoter recognition during transcription initiation.^[11] These proteins bind to the core RNA polymerase, forming a holoenzyme capable of targeting distinct DNA promoter sequences to direct the expression of specific gene sets.^[12] The primary or housekeeping sigma factor, denoted σ⁷⁰ in Escherichia coli and σ^A in many other bacteria, directs transcription from the majority of constitutive promoters under normal growth conditions.^[12] Alternative sigma factors enable responses to environmental stresses by redirecting the holoenzyme to specialized promoters; for instance, σ³² (RpoH) activates heat shock genes to protect against thermal stress and protein misfolding.^[13] Similarly, σ⁵⁴ (also called σ^N or RpoN) regulates genes involved in nitrogen limitation and other nutrient stresses, often requiring enhancer-binding proteins for activation.^[14] These alternative sigmas, including extracytoplasmic function (ECF) types, play crucial roles in adaptive stress responses across bacterial species.^[15] For σ⁷⁰-dependent promoters in E. coli, the core recognition elements are the -10 box (consensus sequence TATAAT) and the -35 box (consensus TTGACA), separated by a spacer of 15-21 base pairs.^[16] These hexameric sequences are contacted by specific domains of the sigma factor, with deviations from consensus reducing promoter strength.^[17] Some σ⁷⁰ promoters feature an extended -10 motif (TGn motif upstream of the -10 box), which enhances recognition in the absence of a strong -35 element.^[17] Strong σ⁷⁰ promoters often include UP elements, AT-rich sequences located upstream of the -35 box that interact with the alpha subunit C-terminal domain of RNA polymerase to increase transcription efficiency.^[18] These elements contribute to high-level expression in highly transcribed genes, such as those for ribosomal RNA.^[19] The binding mechanism involves conserved domains within sigma factors: region 2 primarily recognizes the -10 box through helix-turn-helix motifs that insert into the DNA major groove, while region 4 contacts the -35 box.^[20] Region 3 provides structural linkage between these domains.^[20] This interaction forms the closed promoter complex, where DNA remains double-stranded prior to isomerization.^[21] Sigma factor diversity varies across bacterial phyla; for example, while E. coli encodes about seven sigma factors, some streamlined actinobacterial genomes, such as those of uncultured UBA5794 lineages, contain fewer sigma factors adapted to niche environments.^[22] In contrast, streptomycetes in Actinobacteria can encode dozens of ECF sigmas for complex developmental regulation.^[23] Recent structural and kinetic studies on σ^N (σ⁵⁴) have captured transcription initiation intermediates, revealing that ATPase-driven activation involves limited DNA unfolding as a rate-limiting step for open complex formation.^[24] Anti-sigma factors regulate sigma activity by sequestration; for example, the Rsd protein binds σ⁷⁰ during stationary phase in E. coli, inhibiting its association with core RNA polymerase and favoring alternative sigma utilization.^[25] This mechanism helps shift transcriptional priorities under nutrient limitation.^[26]

Stages of Transcription

Initiation

Bacterial transcription initiation begins with the binding of the RNA polymerase holoenzyme (Eσ), consisting of the core enzyme and a sigma factor, to the promoter DNA, forming a closed promoter complex (RPc). In this initial stage, the DNA remains double-stranded, and specific interactions occur between the sigma factor's recognition domains and the promoter's conserved elements, such as the -10 and -35 boxes in σ70-dependent promoters. This binding is sequence-specific and sets the stage for subsequent conformational changes in both the enzyme and DNA.^[27] The closed complex then undergoes isomerization to form the open promoter complex (RPo), a critical step involving the melting of approximately 14 base pairs of DNA to create a transcription bubble around the start site (+1). This unwinding is driven by the binding free energy of RNAP to the promoter, with an activation energy barrier of about 34 kcal/mol, and does not require helicase activity or NTP hydrolysis in the case of housekeeping sigma factors like σ70; instead, it relies on concerted conformational rearrangements within the RNAP active site cleft that stabilize the single-stranded DNA. Promoter strength is influenced by the spacing between the -10 and -35 boxes, with an optimal length of 17 ± 1 bp facilitating proper alignment and maximizing open complex formation rates; deviations, such as insertions or deletions, or mutations altering sequence conservation, can reduce binding affinity and overall transcriptional efficiency by misaligning the sigma factor domains relative to the DNA helix.^[27]^[28] Following open complex formation, initiation proceeds with the binding of the initiating nucleotides and synthesis of short RNA transcripts during the abortive initiation phase, where RNAP repeatedly produces and releases oligonucleotides of 2-10 nucleotides without promoter clearance. This phase involves DNA scrunching, where the downstream DNA is compacted to accommodate initial RNA-DNA hybrid formation, and is characterized by low processivity until promoter escape occurs. Recent real-time cryo-EM studies have captured key intermediates in σN (σ54)-dependent initiation, revealing paused states such as the early-melted complex (RPem) and translocation intermediates (RPi1) that arise after ATP hydrolysis by enhancer-binding proteins, highlighting how limited unfolding and ~15 ATP hydrolysis cycles drive bubble formation in this alternative pathway.^[29]^[24] Promoter clearance marks the transition to elongation, typically after synthesis of about 10 nucleotides, when the sigma factor is released from the core RNAP, allowing the enzyme to enter a processive elongation mode. This escape requires initial NTP hydrolysis to stabilize the short RNA-DNA hybrid and overcome promoter contacts, ensuring commitment to full-length transcription.^[27]

Elongation

During the elongation phase of bacterial transcription, RNA polymerase (RNAP) synthesizes RNA processively by incorporating nucleotides complementary to the DNA template, advancing along the DNA at rates typically ranging from 20 to 80 nucleotides per second in Escherichia coli, with an average of approximately 42 nucleotides per second under optimal conditions. This phase follows promoter clearance and involves high processivity, allowing RNAP to transcribe thousands of nucleotides without dissociating, though elongation pauses occur at regulatory sites such as pause sequences or roadblocks to facilitate control of gene expression. The translocation of RNAP along the DNA occurs via an inchworm-like mechanism, in which the enzyme maintains stable contacts with the downstream DNA while the catalytic active site, containing an 8–9 base pair RNA-DNA hybrid, progresses forward with the nascent RNA chain.^[30]80180-4) This hybrid stabilizes the transcription elongation complex (TEC) by keeping the RNA 3′ terminus aligned in the active site, preventing slippage and ensuring accurate register during nucleotide addition; disruptions, such as mismatches, can destabilize the hybrid, leading to backtracking where the RNA 3′ end extrudes into the secondary channel.80180-4) Backtracking arrests elongation but enables error correction through intrinsic endonucleolytic cleavage of the extruded RNA, a process enhanced by GreA and GreB factors that stimulate transcript trimming and realign the catalytic register, rescuing stalled complexes with efficiencies up to 60% higher in wild-type cells compared to gre mutants. Fidelity during elongation is maintained by multiple mechanisms, including kinetic proofreading and allosteric regulation that discriminate correct nucleoside triphosphates (NTPs). Kinetic proofreading exploits backtracking to excise mismatched nucleotides via dinucleotide cleavage at the active site, reducing errors by over two orders of magnitude when cleavage rates balance addition rates, with Gre factors coordinating Mg²⁺ ions to boost this activity in backtracked states. Allosteric regulation involves the trigger loop, which folds to stabilize the pre-translocated state and accelerates cognate NTP incorporation by ~10⁴-fold through Watson-Crick base pairing in the closed active site, while rejecting non-cognate NTPs and deoxyribonucleotides via interactions with residues like β′Arg425 and β′Asn458; trigger loop stability modulates both speed and accuracy, with less stable variants enhancing fidelity. Elongation is tightly coupled with translation in bacteria, where ribosomes follow RNAP in real time, coordinating via mRNA looping over hundreds of nucleotides to prevent uncoupled transcription that could form deleterious R-loops.^[31] Recent 2024 single-molecule fluorescence and cryo-EM studies reveal that ribosomes slow upon encountering paused RNAP, rescuing pauses (e.g., NusA-induced) twofold faster and stabilizing the expressome through factors like NusG, thereby maintaining forward progression and avoiding R-loop accumulation upstream of RNAP.^[31] Structural dynamics of elongating RNAP complexes, elucidated by cryo-EM and single-molecule FRET, show the clamp domain—formed by the β and β′ subunits—interconverting dynamically among open, intermediate, and closed states on timescales of 0.1–1 second, facilitating DNA loading and hybrid stability while preventing dissociation.^[32] The clamp's opening and closing motions accommodate the growing RNA-DNA hybrid and respond to stressors like ppGpp, which stabilizes the open state to modulate elongation rates during nutrient limitation.^[32]

Termination

Bacterial transcription termination ensures the precise release of the completed RNA transcript from RNA polymerase (RNAP) and DNA, defining the boundaries of gene expression. This process occurs through two primary mechanisms: intrinsic (Rho-independent) termination, which relies solely on RNA sequence elements, and Rho-dependent termination, which involves the Rho helicase protein. These mechanisms prevent aberrant transcription beyond gene ends and maintain cellular resource efficiency.^[33] Intrinsic termination is triggered by specific RNA structures formed during elongation. The nascent RNA folds into a GC-rich stem-loop (hairpin) structure immediately upstream of a run of 7-8 uridines (U-tract) at the 3' end. The hairpin causes RNAP to pause, destabilizing the weak A-U RNA-DNA hybrid in the active site, leading to dissociation of the transcript, RNAP, and DNA.^[34]^[35] This process requires no additional protein factors and is highly sequence-dependent, with the hairpin forming due to the thermodynamic favorability of GC base pairs.^[33] In contrast, Rho-dependent termination involves the ring-shaped Rho hexamer, an ATP-dependent RNA/DNA helicase that binds to C-rich, unstructured Rho utilization (rut) sites on the nascent RNA, typically 70-90 nucleotides upstream of the termination point. Rho translocates along the RNA in a 5' to 3' direction, using ATP hydrolysis to advance toward the RNAP, where it catches up during pauses and unwinds the RNA-DNA hybrid, dislodging the elongation complex and releasing the transcript.^[36]^[37] This mechanism is crucial for terminating transcription at sites lacking strong intrinsic signals and prevents wasteful synthesis of untranslated RNAs.^[33] The efficiency of both termination types depends on terminator strength, primarily determined by hairpin stability (measured as free energy change, ΔG) and U-tract length in intrinsic terminators. More stable hairpins (lower ΔG) and longer U-tracts enhance dissociation by increasing pausing and hybrid instability.^[38] However, exceptions occur through antitermination, where factors like NusA and NusG modulate RNAP pausing and Rho activity; for instance, NusG can inhibit Rho-dependent termination in certain contexts, such as ribosomal RNA operons, by stabilizing elongation complexes.^[39]^[40] In Bacillus subtilis, Nus factors are essential for overcoming Rho-mediated termination at specific sites.^[37] Recent studies highlight terminators' role in resolving transcription-replication conflicts (TRCs) in bacteria. Directional biases in genome organization, influenced by terminator positions, minimize head-on collisions between RNAP and replisomes, with 2023 research showing that local three-dimensional chromatin structures and termination signals coordinate replication timing to reduce TRC-induced DNA damage.^[41] Rho inhibition has therapeutic implications, as polyaromatic compounds like bicyclomycin act as antibiotics by binding Rho's ATP-binding site, noncompetitively blocking its helicase activity and disrupting Rho-dependent termination, leading to excessive transcription and bacterial cell death.^[42]^[33] Bicyclomycin, produced by Streptomyces species, exemplifies this class and has been structurally validated for its specific interference with Rho translocation.^[43]

Regulation of Transcription

Operons and Negative Control

In bacteria, genes encoding functionally related proteins are often organized into operons, which are clusters of structural genes transcribed as a single polycistronic mRNA under the control of a shared promoter and operator region. This arrangement allows coordinated regulation of gene expression in response to environmental cues. Negative control mechanisms repress transcription initiation or elongation by repressor proteins that bind to operator DNA sequences, thereby inhibiting RNA polymerase activity. The lac operon in Escherichia coli serves as a classic model for negative control, where the lacI gene product, a repressor protein, binds to the operator sequence overlapping the promoter, preventing RNA polymerase from initiating transcription of the lacZYA genes involved in lactose metabolism. In the absence of lactose, the repressor maintains tight repression; however, allolactose, an isomer of lactose, acts as an inducer by binding the repressor and causing a conformational change that reduces its affinity for the operator, allowing transcription to proceed. This model was first proposed by Jacob and Monod based on genetic and biochemical analyses. Repressors can inhibit transcription through direct binding to operator DNA or by requiring a corepressor for activation. For instance, the tetracycline repressor (TetR) from the Tn10 transposon binds as a homodimer to tandem operator sites in the absence of tetracycline, blocking RNA polymerase access to the promoter of tetracycline resistance genes; tetracycline binding induces a structural shift in TetR, releasing it from DNA. Similarly, the trp repressor in E. coli, encoded by trpR, requires tryptophan as a corepressor to bind the operator and repress the trpEDCBA operon, which encodes enzymes for tryptophan biosynthesis; high tryptophan levels thus feedback to inhibit further synthesis.^[44]^[44]^[45]^[45] An additional layer of negative control in amino acid biosynthesis operons, such as trp, involves transcription attenuation, where nascent RNA secondary structures in the leader region sense cellular conditions to terminate transcription prematurely. In the trp operon, the leader transcript contains four regions that can form alternative hairpin structures: a ribosome stalling at tandem Trp codons in a leader peptide coding sequence (when tryptophan is limiting) promotes an antiterminator hairpin, allowing read-through; conversely, abundant tryptophan enables rapid translation, favoring a terminator hairpin that halts elongation before the structural genes. This mechanism fine-tunes expression independently of the trp repressor. Negative control also operates in stress responses, exemplified by the LexA repressor in the SOS regulon, which binds to operator sites (SOS boxes) in promoters of ~40 DNA repair genes across E. coli, maintaining repression under normal conditions; DNA damage triggers RecA-mediated autocleavage of LexA, derepressing the regulon to promote survival. Recent advances in massively parallel reporter assays have mapped repressor binding landscapes at scale, revealing that TetR recognizes a highly rugged sequence space with navigable specificity determinants, enabling precise yet evolvable operator discrimination in bacterial genomes.^[46]^[46]^[47]^[47]

Positive Control and Global Regulators

Positive control mechanisms in bacterial transcription enhance the efficiency of RNA polymerase (RNAP) recruitment, open complex formation, or processivity at specific promoters, often in response to environmental signals. Activators typically bind to upstream DNA sites and make direct protein-protein contacts with RNAP components to overcome rate-limiting steps in initiation. These interactions can be classified based on the position of the activator binding site relative to the promoter: class I sites are located approximately 60 base pairs upstream, where activators contact the C-terminal domain (CTD) of the RNAP alpha subunit to recruit the holoenzyme; class II sites overlap or are adjacent to the -35 promoter element, allowing contact with the beta subunit or sigma factor to stabilize promoter binding.^[48]^[49]^[50] A canonical example is the cAMP receptor protein (CRP), which binds cyclic AMP (cAMP) under glucose-limited conditions to activate catabolite-sensitive promoters like lac. CRP-DNA complexes at class I or II sites stimulate isomerization to the open complex by up to 100-fold, primarily through allosteric changes in RNAP that favor DNA melting. Another activation strategy involves competition among sigma factors for core RNAP, where global signals shift holoenzyme composition to prioritize alternative promoters; for instance, certain activators enhance sigma54-dependent transcription by displacing sigma70.^[51]^[52]^[53] Global regulators exert coordinated effects across the genome, often integrating multiple signals to fine-tune expression. The alarmone ppGpp, synthesized during nutrient stress as part of the stringent response, binds RNAP in concert with the co-regulator DksA to modulate promoter selectivity; while it represses rRNA synthesis, ppGpp-DksA positively activates amino acid biosynthesis operons (e.g., his and trp) and virulence genes in pathogens like Xanthomonas campestris by enhancing open complex formation at sigma70 promoters, increasing expression by 2- to 5-fold. This dual role allows bacteria to redirect resources from growth to survival.^[54]^[55] Antitermination provides a mechanism to extend transcription beyond intrinsic or Rho-dependent terminators, effectively boosting downstream gene expression. In bacteriophage lambda, the N protein binds nut sites on nascent RNA and recruits host Nus factors (NusA, NusB, NusE/S10, and NusG), forming a complex that modifies RNAP's elongation properties to suppress pausing and termination, enabling >90% read-through at multiple terminators for timely viral gene expression. This process illustrates how viral hijacking of bacterial factors achieves positive regulation.^[56]^[57] Two-component systems enable stimulus-specific activation, coupling sensor kinases to response regulators that interface with RNAP. During phosphate starvation, the PhoR kinase autophosphorylates and transfers the phosphate to PhoB, which then dimerizes and binds Pho boxes upstream of target promoters to activate ~50 sigma70-dependent genes involved in phosphate scavenging, such as pst operons, by contacting region 4 of sigma70 to enhance RNAP binding affinity by 10- to 20-fold. This system exemplifies how environmental cues trigger widespread transcriptional reprogramming.^[58]^[59]^[60] Research from 2025 highlights the role of nucleoid organization in global regulation. Transcription-translation coupling (TTC) at promoter-proximal sites prevents RNAP stalling and ensures efficient early transcription and mRNA stability in Escherichia coli. Additionally, transertion actively organizes the nucleoid near the inner membrane during rapid growth (doubling time ~27 minutes), with inhibition of protein biosynthesis causing nucleoid collapse within 10 minutes and influencing spatial correlations with cytoskeletal elements like MreB. These mechanisms link local synthesis to broader genome coordination.^[61]^[62]

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Thus, ppGpp has a positive effect on in vitro dnaK transcription under conditions of competition between σ32 and σ70, but have no observable effect when σ32 ...
[55]
Stringent response regulators (p)ppGpp and DksA positively ...
Oct 17, 2019 · In conclusion, stringent response regulators DksA and (p)ppGpp play an important role in virulence, nutrition uptake and host adaptation of Xcc.
[56]
Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA ...
Apr 20, 2023 · The stringent response is a sensory system widely present in bacteria that can regulate various cellular processes such as fatty acid metabolism ...
[57]
The role of E. coli Nus-factors in transcription regulation and ...
The Nus transcription-factors were originally identified as part of the E. coli phage λ N-protein-controlled antitermination system; hence, they were termed N- ...
[58]
Structural Basis for the Action of an All-Purpose Transcription Anti ...
Apr 4, 2019 · Bacteriophage λN protein, a model anti-termination factor, binds nascent RNA and host Nus factors, rendering RNA polymerase resistant to all pause and ...
[59]
The structure of a transcription activation subcomplex reveals how ...
Aug 9, 2011 · PhoB is a two-component response regulator that activates transcription by interacting with the σ70 subunit of the E. coli RNA polymerase in ...
[60]
Genome-Wide Mapping of the Escherichia coli PhoB Regulon ...
PhoB forms a two-component system with the sensor kinase PhoR (31). When inorganic phosphate (Pi) levels are low, PhoR autophosphorylates and then ...
[61]
Identification of the PhoB Regulon and Role of PhoU in the ...
Dec 14, 2015 · Our work demonstrates that PhoB is induced to regulate nearly 50 genes under phosphate-starved conditions.
[62]
Promoter-proximal transcription–translation coupling controls early ...
The functional coupling of transcription and translation contributes significantly to maintaining messenger RNA (mRNA) expression in bacterial cells.
[63]
The nucleoid of rapidly growing Escherichia coli localizes close to ...
Apr 20, 2025 · In bacteria, they occur simultaneously with other cellular processes, such as transcription, translation or signaling, and share the same space ...