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Intrinsic termination

Intrinsic termination, also known as Rho-independent termination, is a factor-independent mechanism of transcription termination in which RNA polymerase (RNAP) recognizes specific terminator sequences in the DNA template, pauses elongation, forms an RNA hairpin structure, and spontaneously dissociates from the nascent RNA and DNA without requiring additional proteins.^[1] This process is prevalent in bacteria such as Escherichia coli, as well as in viruses and eukaryotic RNA polymerase III (RNAPIII) transcription.^[1]^[2] The terminator sequence typically consists of a GC-rich inverted repeat in the DNA that forms a stable RNA stem-loop hairpin, followed immediately by a run of 6–8 uridines (U-tract) at the 3' end of the nascent RNA.^[3]^[2] Upon reaching the terminator, RNAP pauses at the -2/-1 positions in the transcription bubble, allowing the hairpin to nucleate in the RNA exit channel and propagate, which disrupts the RNA-DNA hybrid by melting at least two base pairs and rewinds the DNA bubble.^[1]^[3] The weak A-U base pairs in the hybrid, combined with hairpin-induced conformational changes in RNAP (such as clamp opening), destabilize the ternary elongation complex, leading to rapid release of the RNA transcript approximately five times faster than the DNA.^[1]^[3] Structural studies using cryo-electron microscopy (cryo-EM) have elucidated the atomic details of this process, revealing intermediate states like the TTC-pause complex (PDB: 7YP9) and TTC-hairpin complex, where the hairpin invades the RNA-binding sites and triggers RNAP reconfiguration.^[1] Unlike Rho-dependent termination, which relies on the Rho helicase protein to catch up to RNAP and unwind the RNA-DNA hybrid at unstructured sites, intrinsic termination depends solely on the intrinsic stability of the RNA structure and the U-tract for efficiency.^[2] The process ensures precise gene expression control by preventing read-through into downstream genes, and its efficiency can be modulated by transcription factors or competing RNA structures like antiterminators.^[1]^[3]

Overview and Context

Definition and Biological Role

Intrinsic termination, also known as rho-independent termination, is a fundamental mechanism in prokaryotic transcription that signals the end of RNA synthesis without the involvement of accessory proteins such as the Rho helicase. It occurs when a GC-rich stem-loop structure, or hairpin, forms in the nascent RNA transcript immediately upstream of a uridine-rich tract (poly-U sequence). This hairpin disrupts the transcription elongation complex, weakening the RNA-DNA hybrid in the polymerase active site and promoting the release of the RNA polymerase (RNAP), nascent RNA, and DNA template.^[4] The process was first characterized in the 1970s through in vitro transcription assays using purified Escherichia coli RNAP on templates derived from bacteriophage lambda and bacterial genes, revealing that termination could proceed efficiently without additional factors. These early studies demonstrated heterogeneous 3'-terminal sequences and the role of RNA secondary structures in halting elongation, laying the groundwork for understanding factor-independent termination pathways. In bacterial gene expression, intrinsic termination plays a critical role by establishing precise 3' ends of mRNA transcripts, which is essential for defining operon boundaries and preventing aberrant read-through transcription into downstream genes. By averting unnecessary elongation, it conserves cellular energy and resources, such as nucleotides and RNAP recycling, thereby optimizing metabolic efficiency in resource-limited environments. This mechanism is particularly vital for operon organization in bacteria like E. coli, where it facilitates coordinated expression of functionally related genes while insulating adjacent transcriptional units from interference.^[5]^[6] Genomic analyses indicate that intrinsic terminators are prevalent, occurring at the ends of approximately 40-50% of transcriptional units or operons in E. coli, underscoring their widespread contribution to transcriptional control across bacterial genomes.^[7]

Comparison to Rho-Dependent Termination

Intrinsic termination and Rho-dependent termination represent the two primary mechanisms of prokaryotic transcription termination, differing fundamentally in their molecular requirements and operational principles. Intrinsic termination operates without accessory proteins, relying instead on specific RNA secondary structures: a GC-rich stem-loop (hairpin) that induces transcriptional pausing in the RNA polymerase (RNAP) elongation complex (EC), followed by a stretch of uridine residues (poly-U tract) that forms weak A-U base pairs with the DNA template, facilitating EC dissociation and RNA release.^[8] In contrast, Rho-dependent termination requires the Rho helicase protein, which binds to C-rich, unstructured regions (rut sites) on the nascent RNA and uses ATP-dependent translocation to catch up with the EC, where it unwinds the RNA-DNA hybrid and dislodges the RNAP.^[9] This protein-mediated process allows Rho to act dynamically on diverse RNA sequences lacking the rigid structural cues of intrinsic terminators.^[10] The trigger factors for these mechanisms further underscore their independence. Intrinsic termination is entirely sequence-encoded within the terminator region, with the hairpin-loop formation and poly-U tract serving as autonomous signals that promote pausing and hybrid instability without external factors.^[11] Rho-dependent termination, however, depends on Rho recruitment to rut sites upstream of the termination point, enabling the helicase to track along the RNA and exert torque on the EC during pauses induced by backtracking or other signals. This reliance on protein-RNA interactions makes Rho-dependent termination responsive to cellular conditions, such as ATP levels, whereas intrinsic termination proceeds predictably based on RNA folding kinetics.^[9] In terms of efficiency and biological contexts, intrinsic termination is generally faster and more deterministic, particularly in leaderless transcripts or at operon ends where precise control is needed, as seen in the efficiency of terminators like λ tR2. It excels in scenarios requiring rapid release without regulatory modulation. Rho-dependent termination, by comparison, is suited to handling polar effects in operons and suppressing pervasive antisense transcription from intergenic regions or foreign DNA, where its flexibility prevents unintended read-through.^[8] Although intrinsic terminators often achieve near-complete termination (>95% in optimal cases), Rho-dependent sites can vary in strength based on rut site accessibility and EC pausing.^[8] Overlap between the mechanisms occurs in some terminators that exhibit features of both; for instance, the attenuator of the trp operon in Escherichia coli is sensitive to Rho. Genome-wide analyses indicate that Rho-dependent terminators comprise 20–50% of transcription terminators in bacteria, with variation by species (e.g., ~20% in E. coli).^[12]^[13]^[14] Evolutionarily, intrinsic termination appears ancestral and is conserved across virtually all bacteria, providing a foundational, protein-independent control layer. Rho-dependent termination, while widespread in most bacterial phyla, is more variable and absent in certain lineages like Mycoplasma and some Cyanobacteria, suggesting it evolved later to enhance regulatory diversity in complex genomes.^[15]

Structural Features

Hairpin Loop and Poly-U Tract

The intrinsic terminator in bacteria features a characteristic RNA hairpin structure formed by an inverted repeat sequence in the nascent transcript. This hairpin consists of a GC-rich stem typically comprising 7-9 base pairs, paired through Watson-Crick interactions, and a small loop of 4-5 nucleotides.^[4] The stem's high GC content confers significant thermodynamic stability, with free energy changes (ΔG) ranging from approximately -10 to -22 kcal/mol, enabling the structure to form rapidly and persist under physiological conditions.^[16] This stability is crucial for the hairpin to act as a physical barrier that disrupts the transcription elongation complex. Immediately downstream of the hairpin lies a poly-U tract, consisting of 6-9 consecutive uridine residues in the RNA, which corresponds to a run of thymidines in the DNA template strand.^[17] The rU-dA hybrid formed between this tract and the DNA template is inherently weak, stabilized by only 2-3 hydrogen bonds per base pair compared to the 3 hydrogen bonds in GC pairs, facilitating hybrid destabilization and polymerase release.^[4] The poly-U tract typically follows immediately after the hairpin (with 0-2 nucleotides spacer), enabling coordinated action without interference.^[1] Sequence analysis of bacterial genomes, particularly in Escherichia coli, has revealed a consensus motif for the stem-loop region, often represented as a GC-rich dyad symmetry, reflecting the inverted repeat pattern that promotes hairpin formation.^[18] This consensus is derived from statistical evaluation of validated terminators and underscores the preference for G/C pairing in the stem to maximize stability. Variability in these elements influences termination efficiency; for instance, interruptions in the stem such as bulges or mismatches reduce hairpin stability and weaken termination, while shortening the poly-U tract to fewer than 6 uridines diminishes hybrid instability.^[4] Functional validation through mutagenesis studies, such as those on the E. coli trp or his operon terminators, demonstrates that altering GC content in the stem or length of the U-tract abolishes termination in reporter gene assays, leading to increased read-through transcription.^[8] These experiments confirm the hairpin and poly-U tract as indispensable core components for intrinsic termination.

Experimental Methods for Identification

Early experimental identification of intrinsic terminators relied on in vitro runoff transcription assays using purified Escherichia coli RNA polymerase on DNA templates derived from bacteriophage lambda, such as plasmids containing the tR1 terminator sequence. In these assays, transcription was initiated upstream of the terminator, allowing the polymerase to produce discrete RNA products that terminated at specific sites, which were then separated and visualized by polyacrylamide gel electrophoresis to confirm termination positions and efficiency.^[19] To map the structural elements involved, such as the RNA hairpin, footprinting and chemical probing techniques were employed. RNase T1 protection assays, which cleave single-stranded guanosine residues, revealed protected regions indicative of hairpin formation in the nascent RNA within the RNA polymerase complex, demonstrating how the secondary structure stabilizes pausing. Similarly, dimethyl sulfate (DMS) probing targeted unpaired adenines and cytosines, highlighting base-pairing patterns in the hairpin loop of intrinsic terminators. Hydroxyl radical footprinting further visualized polymerase pausing by generating radicals that cleave exposed DNA backbone segments, showing enhanced protection at terminator sites where the enzyme stalls, thus linking pausing to hairpin invasion.^[20]^[21] In vivo validation of intrinsic termination involved reporter gene fusions, such as placing the lacZ gene downstream of a terminator sequence to quantify efficiency through β-galactosidase activity levels; reduced activity indicated high termination, as fewer full-length transcripts reached the reporter. Transcript mapping via Northern blotting complemented this by hybridizing probes to cellular RNA, identifying terminated products and confirming site-specific 3' ends in bacterial extracts.^[22] Modern high-throughput methods have enabled genome-wide characterization. Term-seq uses deep sequencing of ligated 3' RNA ends from bacterial libraries to map thousands of terminators simultaneously, revealing their sequences and efficiencies across conditions. Cryo-electron microscopy (cryo-EM) structures from 2023 resolved paused RNA polymerase complexes at intrinsic terminators, visualizing hairpin formation and its invasion into the enzyme's RNA exit channel at near-atomic resolution.^[1] Termination efficiency is typically calculated as the percentage of terminated transcripts relative to total transcripts produced, often reaching 80-95% for strong intrinsic terminators under optimal in vitro or in vivo conditions.^[23]

Termination Mechanism

Step-by-Step Process

Intrinsic termination in bacteria proceeds through a coordinated sequence of molecular events during the final stages of transcription elongation by RNA polymerase (RNAP). The process is triggered by the transcription of specific terminator sequences in the DNA template, which encode an RNA hairpin followed by a polyuridine (poly-U) tract. This leads to the destabilization and eventual dissociation of the elongating transcription complex (EC).^[3] The process begins with Step 1: Transcription of the terminator sequence. As RNAP elongates, it transcribes the GC-rich inverted repeat that forms the stem of the RNA hairpin, along with the initial portion of the downstream poly-U tract. This results in the formation of an initial 8-9 base pair RNA-DNA hybrid within the polymerase active site, where the newly synthesized RNA pairs with the template DNA strand. The structural elements of the hairpin loop and poly-U tract enable the subsequent folding and hybrid weakening necessary for termination.^[3] In Step 2: Pausing and hairpin formation, RNAP pauses at the -2/-1 positions within the transcription bubble upon reaching the terminator, adopting a half-translocated state. The transcribed RNA sequence then folds into a stable GC-rich hairpin structure that nucleates in the RNA exit channel of RNAP. The hairpin propagates, invading the RNA-binding sites and melting 4-5 base pairs of the upstream RNA-DNA hybrid while rewinding the DNA bubble. This disrupts the hybrid and disengages the RNA from the active site. Cryo-EM structures reveal key intermediates such as the TTC-pause complex (PDB: 7YP9) and TTC-hairpin complex, highlighting the hairpin's role in triggering RNAP reconfiguration.^[1]^[24] Step 3: Weakening of the rU-dA hybrid by poly-U tract transcription overlaps with hairpin formation, as RNAP incorporates additional uridine residues from the poly-U tract into the hybrid. The rU-dA base pairs are inherently weak due to fewer hydrogen bonds compared to GC pairs, which increases the off-rate of RNAP from the DNA template and further promotes hybrid instability. This step amplifies the disruptive effects initiated by the hairpin, facilitating the release of the RNA transcript.^[3] Finally, Step 4: Conformational change and dissociation occurs, involving structural rearrangements in RNAP, including clamp opening, that destabilize the ternary complex. The hairpin clashes with elements like the trigger loop, enlarging the RNA exit channel and blocking re-elongation. This leads to the complete separation of RNAP from the DNA and RNA, releasing the fully terminated transcript, with RNA dissociating approximately five times faster than DNA. The β-flap accommodates the hairpin during this process.^[1]^[24] Key intermediates in this process include the pre-termination complex, where the hairpin-bound RNAP remains associated with the DNA but with a disrupted hybrid, and the post-termination complex, consisting of free RNAP and the released RNA molecule. Single-molecule Förster resonance energy transfer (FRET) studies have revealed that termination is efficient within 10-20 nucleotides after the U-tract, highlighting the rapid progression from hairpin formation to dissociation.^[24]

Biophysical and Thermodynamic Principles

The biophysical principles underlying intrinsic termination in bacterial transcription revolve around the relative stabilities of the RNA-DNA hybrid and the nascent RNA hairpin structure within the RNA polymerase (RNAP) elongation complex (EC). The RNA-DNA hybrid in the active site typically consists of 8-9 base pairs, but at intrinsic terminators, the downstream poly-U tract forms rU-dA pairs that are inherently weaker than standard Watson-Crick pairs. These rU-dA pairs exhibit a lower melting temperature (Tm ≈ 40°C) compared to rA-dT pairs (Tm ≈ 50°C), with each rU-dA pair contributing a free energy change (ΔG) of approximately -1 to -2 kcal/mol less stability than rA-dT equivalents, facilitating hybrid destabilization and EC dissociation.^[25]^[26] The thermodynamics of hairpin formation further drive termination efficiency, as calculated using nearest-neighbor models such as the Mathews algorithm for RNA folding free energy (ΔG_hairpin). Strong terminators feature hairpins with ΔG_hairpin ≈ -17 to -14 kcal/mol, which correlates with >90% termination efficiency by outcompeting the hybrid for base-pairing interactions and providing sufficient energetic favorability to invade the RNAP active site.^[27] This energetic competition is captured in a simplified partitioning model for termination probability:

P = \frac{1}{1 + e^{(\Delta G_{\text{hybrid}} - \Delta G_{\text{hairpin}})/RT}}

where ΔG_hybrid is the free energy of the RNA-DNA hybrid, ΔG_hairpin is the hairpin folding free energy, R is the gas constant, and T is the temperature in Kelvin; this logistic form arises from thermodynamic models balancing elongation versus release pathways.^[28] Kinetically, intrinsic termination follows a two-state dissociation model, transitioning from a paused EC to a fully terminated state, with the hairpin accelerating the off-rate constant (k_off) by approximately 10^3-fold relative to hairpin-free pausing, as revealed by optical tweezers measurements of force-dependent EC stability.^[29] Allosterically, the invading hairpin clashes with the RNAP trigger loop, inducing domain motions that enlarge the RNA exit channel, enhance NTP hydrolysis at the active site, and block re-elongation by locking the complex in a pre-translocated, inactive conformation.^[30]

Regulation and Modulation

Intrinsic Factors Affecting Efficiency

The efficiency of intrinsic termination in bacteria is modulated by several sequence-intrinsic features of the terminator structure, primarily the stability of the RNA hairpin and the properties of the adjacent U-tract, without involvement of external factors. The GC content within the hairpin stem plays a critical role, as higher GC pairing enhances the thermodynamic stability (more negative ΔG) of the structure, thereby increasing termination efficiency. For instance, stems with 8-10 GC base pairs can achieve up to 95% efficiency by promoting rapid hairpin formation that disrupts the RNA-DNA hybrid.^[31] In contrast, mismatches or bulges in the stem reduce stability and termination efficiency by 20-50%, as they weaken base pairing and slow the folding kinetics necessary for polymerase release.^[23] The length and composition of the U-tract immediately downstream of the hairpin are equally important determinants of efficiency. Optimal U-tracts consist of 7-8 consecutive uridines, which form weak rU-dA base pairs in the transcription bubble, facilitating hybrid destabilization and RNA release with efficiencies often exceeding 90%.^[31] Shorter U-tracts (fewer than 6 uridines) significantly impair termination, dropping efficiency below 50% due to insufficient weakening of the hybrid.^[32] Conversely, excessively long U-tracts (more than 10 uridines) can lead to polymerase slippage or alternative pausing, potentially reducing precise termination.^[31] The sequence context upstream of the terminator also influences efficiency by affecting the timing of hairpin formation relative to polymerase progression. GC-rich sequences immediately upstream promote transcriptional pausing, providing additional time for the nascent RNA to fold into the stable hairpin before the U-tract is transcribed, thereby enhancing overall termination.^[33] AT-rich upstream leaders, however, can accelerate elongation and hinder hairpin assembly, weakening termination.^[31] Intrinsic terminators are classified by strength based on these sequence features, with strong terminators exhibiting near-complete termination (e.g., the λtI terminator with 95-99% efficiency due to its robust GC-rich stem and U-tract) and weak ones showing partial read-through (e.g., 60-80% efficiency in some ribosomal operons like the E. coli β-β′ operon, where tuned termination allows differential expression of downstream genes).^[34] Strong terminators, such as those with uninterrupted high-GC stems and optimal U-tracts, predominate at operon ends to ensure clean transcript separation.^[4] Weaker terminators, often with suboptimal stems or U-tracts, are distributed internally within operons to enable conditional read-through and fine-tune gene expression ratios under varying conditions.^[31]

Extrinsic Regulatory Mechanisms

Extrinsic regulatory mechanisms modulate intrinsic termination through interactions with RNA polymerase (RNAP), the nascent RNA, or environmental signals, allowing bacteria to fine-tune gene expression in response to cellular conditions. One key protein factor is NusA, which binds to RNAP near the RNA exit channel and stabilizes interactions between the forming terminator hairpin and RNAP, thereby promoting pause extension and facilitating hairpin invasion of the RNAP-RNA hybrid.^[35] In vitro studies demonstrate that NusA increases termination efficiency at select intrinsic terminators by 2- to 5-fold, primarily by destabilizing upstream RNA-protein contacts that hinder hairpin folding.^[35] This enhancement is particularly evident at terminators like λ tR2, where NusA boosts the percentage of terminated transcripts without altering the core termination signal sequence.^[35] Similarly, the elongation factor NusG functions as an intrinsic termination factor that stimulates termination at many sites, acting alone or cooperatively with NusA to enhance efficiency.^[36] Small molecules such as the alarmone ppGpp also exert control during the stringent response to nutrient stress, binding directly to RNAP to induce conformational changes that slow elongation and promote pausing.^[37] These shifts favor intrinsic termination at GC-rich pause sites by allowing more time for terminator hairpin formation and hybrid destabilization, particularly in operons requiring rapid downregulation.^[37] For instance, ppGpp significantly elevates termination efficiency at the rrnB T1 intrinsic terminator, linking global transcription reprogramming to survival under starvation.^[37] Attenuator systems provide translation-coupled regulation of intrinsic termination, as seen in amino acid biosynthesis operons like trp and his, where the position of the translating ribosome dictates alternative RNA folding outcomes.^[38] Under high tryptophan levels, rapid translation of the trp leader peptide covers segments of the nascent RNA, permitting formation of a terminator hairpin and premature transcription halt; conversely, low tryptophan stalls the ribosome, exposing sequences that form an antiterminator hairpin instead, enabling readthrough into structural genes.^[38] Similar dynamics operate in the his operon, where histidine availability modulates ribosome progression to toggle between terminator and antiterminator structures, ensuring coordinated expression based on amino acid pools.^[38] Small regulatory RNAs (sRNAs) influence intrinsic termination by base-pairing with nascent transcripts to disrupt terminator hairpin formation, often during stress adaptation. Temperature serves as an extrinsic cue in some bacteria, where elevated conditions reduce the stability of the terminator hairpin due to weakened base-pairing, thereby impairing termination efficiency and promoting read-through to upregulate gene expression.

Inhibitors and Antiterminators

Molecular Inhibitors

Molecular inhibitors of intrinsic termination encompass proteins, small molecules, and RNA elements that disrupt the formation or function of terminator hairpins and the subsequent RNAP dissociation at poly-U tracts. Natural antiterminators, such as the bacteriophage λ N protein, exemplify this by binding to the boxB RNA hairpin within the nascent transcript of phage genes. This interaction recruits host factors like NusA, NusE, and NusG to remodel the RNAP elongation complex, obstructing hairpin folding in the RNA exit tunnel and stabilizing the transcription bubble to prevent pausing and termination.^[39] Synthetic inhibitors like streptolydigin target RNAP directly to inhibit transcription elongation, which impacts pausing and may indirectly affect intrinsic termination. Streptolydigin binds adjacent to the active center, primarily interacting with the bridge helix in the β' subunit, stabilizing a straight bridge-helix conformation that inhibits translocation and favors non-backtracked states, thereby preventing conformational changes during elongation; the inhibition constant (K_i) for elongation is approximately 1.8 μM in Thermus thermophilus RNAP.^[40] Riboswitches provide another layer of inhibition through ligand-dependent RNA restructuring. In the TPP riboswitch, binding of thiamine pyrophosphate induces a conformation that sequesters the terminator hairpin sequence, favoring an antiterminator structure and reducing termination efficiency by up to 70% in reporter assays, thereby allowing read-through transcription under high metabolite conditions.^[41] Engineered systems leverage these principles for controlled antitermination. BoxB hairpin mimics, derived from phage λ, can be inserted into synthetic transcripts to recruit NusG and associated factors, counteracting terminator signals by modifying RNAP processivity in biotechnological constructs. In pathological contexts, mutations in the rpoB gene conferring rifampicin resistance indirectly perturb termination. These alterations in the RNAP β subunit disrupt interactions with NusA and affect the efficiency of both intrinsic termination and λ N-mediated antitermination, often leading to altered pausing and release kinetics at terminator sites.^[42]

Applications in Biotechnology

Synthetic terminators engineered based on intrinsic termination motifs, such as stable hairpin loops followed by poly-U tracts, are essential for optimizing gene expression in bacterial biotechnology applications. The BBa_B0015 double terminator, registered in the iGEM parts registry, combines an Escherichia coli rrnB terminator (BBa_B0010) with a T7 phage terminator (BBa_B0012) to achieve high-efficiency transcription termination, thereby enhancing plasmid stability and reducing leaky expression in E. coli systems. This part has been integrated into modular toolkits like EcoFlex for synthetic biology, where it maintains consistent reporter gene output, such as GFP fluorescence, across diverse genetic constructs with less than 2.5-fold variation.^[43]^[44] In CRISPR-Cas9 genome editing, intrinsic terminators are incorporated into guide RNA (gRNA) expression units to ensure clean termination of Pol III transcription and mitigate off-target effects from transcriptional read-through. The standard gRNA scaffold features a poly-T tract acting as a terminator, which signals RNA polymerase III to stop immediately after the gRNA sequence, preventing aberrant extensions that could generate non-specific RNAs or reduce editing precision. Optimizations, such as fine-tuning poly-T length, have improved gRNA transcript levels and on-target efficiency in mammalian cells by up to 50% without increasing off-target activity.^[45] Riboswitch-terminator fusions leverage intrinsic termination for developing sensitive biosensors that detect metabolites and trigger reporter gene expression. For adenine detection, the addA riboswitch from Vibrio vulnificus, when fused to a transcriptional terminator and upstream of a GFP reporter in E. coli, undergoes conformational change upon adenine binding to disrupt the terminator stem-loop, allowing read-through transcription and fluorescence activation with a dynamic range of approximately 15-fold. These constructs, enhanced by ribo-attenuators, reduce expression variability.^[46] Weak intrinsic terminators are applied in attenuated bacterial vaccines to modulate virulence gene expression, balancing safety and immunogenicity. Recent advances in the 2020s include machine learning models, such as iTerm-PseKNC, which predict terminator efficiency from sequence features with over 90% accuracy, and databases like WebGeSTer DB, facilitating the design of custom terminators for precise genome editing and synthetic circuits.^[47]^[48]

Extensions to Other Domains

Features in Archaea

In archaea, intrinsic transcription termination exhibits core similarities to the bacterial mechanism, relying on sequence elements that destabilize the transcription elongation complex (TEC). These terminators typically feature a stretch of 5 to 10 adenines (oligo(dA)) in the template DNA strand, corresponding to oligo(dT) in the nontemplate strand, which encodes a polyuridine (poly(U)) tract at the 3' end of the nascent RNA, forming weak rU:dA RNA-DNA hybrids that promote RNAP release.^[49] For instance, in the thermoacidophilic archaeon Sulfolobus, intrinsic terminators have been identified downstream of genes.^[49] Archaeal intrinsic termination displays unique adaptations shaped by genome composition and transcription machinery. Poly(T) tracts are less prevalent in archaea due to their generally AT-poor genomes, leading to sparser but functional U-tracts that often require multiple short runs (e.g., U4 motifs) for robust activity; in Methanococcus maripaludis, transcription units with more than two U4-tracts exhibit significantly higher termination efficacy compared to those lacking them.^[50] Additionally, while GC-rich hairpins can occur in some archaeal terminators, they are not essential, distinguishing this process from the canonical bacterial rho-independent model that mandates a stable stem-loop upstream of the U-tract.^[51] Genome-wide Term-seq analyses in Methanococcus maripaludis have mapped over 2,300 transcription termination sites, revealing that intrinsic signals, particularly U-tracts, cluster at operon boundaries and often function bidirectionally to prevent read-through transcription into intergenic or antisense regions.^[52] These terminators are enriched downstream of stop codons, with termination efficacy positively correlating with U-tract density, underscoring their role in precise transcript delineation.^[52] Evolutionarily, archaeal intrinsic termination bridges prokaryotic and eukaryotic paradigms, as archaeal RNA polymerase shares structural homology with eukaryotic RNA polymerase II, enabling hybrid mechanisms where poly(U)-driven release integrates with factor-assisted processes like those involving aCPSF1, a U-tract-binding protein that boosts efficiency by cleaving nascent RNA ends.^[50] This conservation highlights adaptations in archaea to suit compact, operon-based genomes while foreshadowing eukaryotic polyadenylation-independent termination modes.

Analogous Processes in Eukaryotes

In eukaryotic transcription, RNA polymerase II (Pol II) pausing at the 3' ends of genes exhibits parallels to bacterial intrinsic termination, where nascent RNA structures play a role in destabilizing the transcription complex, although eukaryotic processes are more tightly coupled to RNA processing. However, the primary mechanism for resolving these paused complexes and ensuring efficient termination relies on the Rat1 (in yeast) or Xrn2 (in mammals) 5'-3' exonucleases, which degrade the nascent RNA from the 5' end after cleavage, "torpedoing" the polymerase away from the template.^[53] A key intrinsic-like element in eukaryotic mRNA termination is the polyadenylation signal, typically the hexanucleotide AAUAAA located 10-30 nucleotides upstream of the cleavage site in the pre-mRNA. The resulting cleavage of the pre-mRNA at the polyadenylation site by the cleavage and polyadenylation specificity factor (CPSF) complex, followed by addition of the poly(A) tail, promotes Pol II termination through recruitment of termination factors.^[54] These events ensure coordinated 3' end formation. The efficiency of this process is bolstered by factors such as the Integrator complex, which binds to RNA hairpins or stem-loop structures near gene ends to cleave nascent transcripts and facilitate Pol II release.^[55] In protein-coding genes, Integrator associates with paused Pol II, promoting rapid cleavage that prevents read-through transcription and enhances overall termination fidelity.^[56] For non-coding RNAs like small nuclear RNAs (snRNAs), terminator hairpins are critical for precise 3' end processing and termination. In U1 snRNA genes, for instance, a specific stem-loop structure known as the 3' box forms immediately after the mature 3' end sequence, serving as a binding site for the Integrator complex to direct endonucleolytic cleavage and subsequent exonucleolytic trimming, ensuring accurate maturation without polyadenylation.^[57] These hairpins not only demarcate the termination point but also couple transcription cessation to snRNP assembly, preventing aberrant extension of the transcript. Eukaryotic RNA polymerase III (Pol III) employs an intrinsic termination mechanism analogous to bacterial systems, relying on terminator sequences consisting of four or more thymidines (oligo(dT)) in the DNA template, which encode poly(U) tracts in the nascent RNA. These weak rU:dA hybrids cause Pol III pausing and release without requiring additional factors, ensuring precise termination for short non-coding RNAs like tRNAs and 5S rRNA. Efficiency is enhanced by the polymerase's intrinsic RNase activity, mediated by subunits like Rpo12 (TFIIS-like), which cleaves backtracked RNA to facilitate dissociation.^[58]^[59]

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The Elongation-Termination Decision in Transcription - Science
Elongation complexes are stable at nonterminator positions; a model is presented to explain the destabilization of these complexes at intrinsic termination ...
[29]
Applied force reveals mechanistic and energetic details of ...
Intrinsic transcription termination ... For each terminator U-tract, the TE increased with load on the RNA (Figure 4A-C), in accordance with a two-state Boltzmann ...
[30]
An Allosteric Path to Transcription Termination - ScienceDirect.com
Dec 28, 2007 · ... β flap; violet, β′ lid; blue, β′ zipper; green, zinc finger; rose ... intrinsic termination, an element that appears to be required by ...
[31]
https://doi.org/10.1016/j.mib.2024.102557
[32]
Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic ... - NIH
Apr 8, 2014 · Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal ...<|control11|><|separator|>
[33]
Trigger loop dynamics can explain stimulation of intrinsic termination ...
Oct 16, 2017 · Termination prevents unwanted gene expression (1), recycles RNAP for new initiation events (2), and prevents genome-destabilizing collisions ...
[34]
Sequences required for transcription termination at the intrinsic λtI ...
The efficiency of λtI was estimated at 95%-99% in vivo, measured by levels of galactokinase (galK) activity (Montañez et al. 1986; Cisneros et al. 1996), and at ...
[35]
https://www.cell.com/cell/fulltext/S0092-8674(01)00582-7
[36]
Regulation of Bacterial Gene Expression by Transcription Attenuation
The trp leader terminator hairpin is only 40% G+C rich, which should make the trp attenuator a weak transcription terminator. However, transcription termination ...
[37]
An RNA thermosensor controls expression of virulence genes in ...
In Listeria monocytogenes, virulence genes are maximally expressed at 37 degrees C, almost silent at 30 degrees C and controlled by PrfA.
[38]
https://pmc.ncbi.nlm.nih.gov/articles/PMC6710462/
[39]
https://doi.org/10.1016/j.molcel.2019.01.016
[40]
https://doi.org/10.1016/j.cell.2005.07.017
[41]
Transcriptional approaches to riboswitch studies - PMC - NIH
The following assay is designed for a quick assessment of the intrinsic termination efficiency as a function of riboswitch activity (Fig. 3, last two lanes) ...
[42]
https://doi.org/10.1016/0022-2836(88)90573-6
[43]
Part:BBa B0015 - parts.igem.org
Jul 17, 2003 · BBa_B0015 is a composite terminator made by joining 2 other terminators, one derived from E. coli (BBa_B0010) and the other from the T7 phage ( ...
[44]
EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology
Apr 20, 2016 · The signal intensity of GFP varied between the constructs but remained within a 2.5-fold range of the BBa_B0015 control plasmid. Interestingly, ...
[45]
CRISPR Guide - Addgene
This guide will provide a basic understanding of CRISPR biology, introduce the various applications of CRISPR, and help you get started using CRISPR in your ...
[46]
Ribo-attenuators: novel elements for reliable and modular riboswitch ...
These five attenuators are used with the addA riboswitch to express sfGFP and OmpT, demonstrating that ribo-attenuators can reduce expression variability (which ...Missing: biosensors | Show results with:biosensors
[47]
Regulation of Bacterial Gene Expression by Transcription Attenuation
Jul 3, 2019 · A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination.
[48]
iTerm-PseKNC: a sequence-based tool for predicting bacterial ...
In this study, we developed a new predictor called 'iTerm-PseKNC' based on support vector machine to identify transcription terminators.
[49]
WebGeSTer DB—a transcription terminator database - PMC - NIH
The database comprises of a million terminators identified in 1060 bacterial genome sequences and 798 plasmids.
[50]
Transcription Regulation in Archaea | Journal of Bacteriology
Jun 27, 2016 · Archaeal intrinsic termination is characterized by a run of 5 to 10 thymidine residues in the nontemplate strand, encoding a poly(U) run at the ...
[51]
aCPSF1 cooperates with terminator U-tract to dictate archaeal ...
Dec 29, 2021 · A bacteria-like intrinsic termination mechanism that depends on a U-stretch is also found in the eukaryotic RNA polymerase (RNAP) III (Nielsen ...
[52]
Archaeal intrinsic transcription termination in vivo - PubMed - NIH
Archaeal transcription termination is stimulated by oligo(T) sequences and is different from the RNA hairpin-dependent mechanism established for intrinsic ...
[53]
aCPSF1 cooperates with terminator U-tract to dictate archaeal ...
Dec 29, 2021 · Recently, Term-seq, an approach that enables accurate mapping of all exposed RNA 3′-ends in prokaryotes and determines the transcription ...
[54]
The structure and activities of the archaeal transcription termination ...
Aug 2, 2022 · While intrinsic termination sequences are often encoded downstream of genes and operons, intrinsic termination signals embedded within the 5′ ...
[55]
Clusters of hairpins induce intrinsic transcription termination ... - Nature
Aug 10, 2021 · We can correctly identify that around three-fourths of all microbial operons/single genes have ITT sites without a bias towards the GC base ...
[56]
Transcriptional termination in mammals: Stopping the RNA ... - NIH
Jun 10, 2016 · The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. ... Xrn2 function in widespread premature termination ...
[57]
Ending the message: poly(A) signals then and now - PMC
Polyadenylation [poly(A)] signals (PAS) are a defining feature of eukaryotic protein-coding genes. The central sequence motif AAUAAA was identified in the mid- ...
[58]
Context-specific regulation and function of mRNA alternative ...
Jul 7, 2022 · RNA polymerase II (Pol II) transcribes DNA and produces pre-mRNAs that are processed into mature mRNAs. The processing steps include capping, ...
[59]
Integrator enforces the fidelity of transcriptional termination at protein ...
Nov 3, 2021 · Integrator directly binds and terminates protein-coding transcripts enriched in alternative polyadenylation sequences.
[60]
Structural basis of Integrator-mediated transcription regulation
Nov 11, 2021 · Pagano, The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res. 25, 288–305 (2015) ...
[61]
Transcription termination by nuclear RNA polymerases - PMC
This review describes advances in our understanding of transcription termination of all three RNAPs, particularly in human and in yeast.