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Group II intron

Group II introns are a class of large, self-splicing ribozymes and mobile genetic elements that catalyze their own excision from precursor RNA transcripts through a two-step transesterification mechanism, generating a lariat-structured intron and ligated exons without requiring protein cofactors, though they frequently associate with intron-encoded proteins to enhance efficiency.^[1] These introns typically range from 400 to 1,500 nucleotides in length and are phylogenetically widespread in bacterial genomes as well as in the mitochondria and chloroplasts of fungi, algae, plants, and some metazoans, and recently discovered in bacteriophage genomes, but are notably absent from most nuclear genomes.^[2]^[3] The conserved secondary structure of group II introns consists of six double-helical domains (I–VI) emanating from a central wheel, with domain V forming the catalytic core that coordinates magnesium ions essential for phosphodiester bond cleavage and formation.^[4] Domain VI contains the bulged adenosine that serves as the branch point for lariat formation during the first splicing step, while many group II introns include an open reading frame in domain IV encoding a multifunctional intron-encoded protein (IEP) that acts as a reverse transcriptase, maturase, and sometimes endonuclease to promote RNA folding, splicing, and mobility.^[1] Splicing proceeds via exon binding sites (EBS) in the intron pairing with complementary intron binding sites (IBS) in the flanking exons, followed by conformational dynamics including protonation-driven toggling of catalytic elements to transition between steps.^[4] Beyond splicing, group II introns exhibit retrotransposition via a target-primed reverse transcription mechanism, where the spliced intron RNA reverse splices into a target DNA site and uses its IEP's reverse transcriptase to copy the RNA into DNA, enabling invasion of new genomic locations.^[2] This mobility, combined with horizontal transfer, has contributed to their broad distribution and diversification into subgroups (e.g., IIA, IIB, IIC based on RNA structure). Evolutionarily, group II introns are considered ancestral to eukaryotic spliceosomal introns, with structural and mechanistic parallels—such as the lariat intermediate and active site motifs—suggesting that components like the U2, U5, and U6 small nuclear RNAs derived from fragmented group II intron domains during the transition to protein-assisted splicing in eukaryotes.^[1] Structural studies, including recent cryo-EM and X-ray crystallography as of 2025, have illuminated these dynamics, highlighting their versatility for biotechnological applications like gene targeting.^[4]^[5]

Structure

Secondary Structure Domains

Group II introns are characterized by a conserved secondary structure consisting of six helical domains (DI–DVI) that radiate from a central core, forming a wheel-like arrangement essential for their ribozyme function. This model was first proposed through comparative sequence analysis of fungal mitochondrial introns, revealing extensive base-pairing homologies that define the domains' stems, loops, and linkers.^[6] Domain I (DI) serves as the largest and most elaborate scaffold, comprising approximately half the intron length and organizing the overall architecture through multiple subdomains with paired helical stems (e.g., P1 through P10) and interconnecting linkers.^[7] Within DI, key base-pairing motifs include the exon-binding sites (EBS1, EBS2, and sometimes EBS3), which form Watson-Crick helices with complementary intron-binding sites (IBS1, IBS2, IBS3) on the flanking exons to ensure precise splice-site recognition. For instance, EBS1-IBS1 pairing aligns the 5' splice site, while EBS2-IBS2 and EBS3-IBS3 interactions position the 3' splice site in subgroups that utilize them.^[8] Domain II (DII) features a prominent helical stem-loop structure with a catalytic bulge and variable linker regions, often accommodating insertions that contribute to structural flexibility without disrupting core pairing. Domain III (DIII) is a short, conserved stem-loop that bridges DI and DIV, stabilizing the central hub via its single helix and internal loop.^[6] Domain IV (DIV) extends as a long, variable arm with helical stems and a large terminal loop that frequently harbors insertions, including open reading frames encoding intron-encoded proteins in mobile variants. Domain V (DV) is the most phylogenetically conserved element, forming a compact stem-loop with two helices separated by a catalytic two-nucleotide bulge (typically AG or AC) and an internal loop containing a triad of nucleotides (e.g., AGC) critical for active site formation through base pairing.^[7] Domain VI (DVI) consists of a short stem-loop with a bulged adenosine serving as the branch-point residue for lariat formation, connected by flexible linkers to the 3' splice site.^[8] Structural variability across the three main subgroups—IIA, IIB, and IIC—primarily manifests in domain lengths and insertions, while preserving the core helical patterns. Subgroup IIA introns, common in bacterial and organellar genomes, exhibit more complex architectures with additional stems and larger insertions in DII and DIV, often exceeding 900 nucleotides in total length. In contrast, IIB introns simplify DII and incorporate an extended EBS3-IBS3 pairing for 3' exon recognition, maintaining similar overall sizes. Subgroup IIC, prevalent in prokaryotes, represents a more primitive and compact form (~400 nucleotides), with reduced DII complexity, fewer insertions in DIV, and distinct EBS/IBS motifs adapted for insertion at specific genomic sites like terminators.^[8] These variations highlight the evolutionary adaptability of the secondary structure while underscoring the invariance of DI, DV, and DVI as functional cornerstones.^[7]

Tertiary Interactions and Folding

The three-dimensional architecture of group II introns is assembled through a network of long-range tertiary interactions that pack the six secondary structure domains into a compact, catalytically active conformation. Domain I (DI) serves as the central scaffold, with its subdomains connected by key contacts such as the kappa-zeta (κ-ζ) and eta-gamma (η-γ) interactions. The κ-ζ interaction involves a tetraloop-receptor pairing between the κ loop in DI(ii) and the ζ receptor in DI, stabilizing the overall shape of DI and acting as a rate-limiting element for intron folding in the ai5γ group IIB intron.^[9] Similarly, the η-γ interaction links the η tetraloop of DVI to the γ receptor in DI, positioning DVI approximately 20 Å from the catalytic core in its "silent" state and facilitating domain docking.^[9] These interactions, conserved across group II intron subgroups, ensure the precise alignment of exon-binding sites and the catalytic domains.^[10] In domain VI (DVI), tetraloop-receptor pairings further reinforce the tertiary fold. The η-η′ interaction between the DVI tetraloop and a receptor in DII, along with the π-π′ contact, stabilizes DVI in both branching and ligation conformations, enabling substrate exchange during splicing.^[10] These pairings are particularly prominent in group IIB introns, where they adopt a GANC tetraloop motif that enhances structural rigidity compared to the GNRA loops in group IIC introns.^[11] Crystal structures of group IIC introns, such as the Oceanobacillus iheyensis intron at 3.1 Å resolution, reveal how these tetraloops dock into distorted A-minor motifs, contributing to the overall compactness.^[12] Magnesium ions play a crucial role in coordinating RNA folding by neutralizing phosphate repulsion and bridging key junctions. At the JII/III junction in DI, a bridging Mg²⁺ ion stabilizes the coordination loop, aligning the EBS1 and EBS3 recognition sites for exon binding and supporting active site formation.^[9] High-resolution structures identify multiple Mg²⁺ binding sites, including two inner-sphere ions (M1 and M2) in the D5 bulge that coordinate the scissile phosphate, with concentrations of 100 mM MgCl₂ required for optimal folding in vitro.^[12] These ions facilitate the transition from open to compact states, as evidenced by hydroxyl radical footprinting experiments showing Mg²⁺-dependent protection of tertiary contact regions.^[11] Structural studies from the Pyle laboratory in the 2010s have provided atomic-level insights into these folds using X-ray crystallography and cryo-EM. For group IIB introns like ai5γ, a 2014 model based on the O.i. group IIC crystal structure (PDB: 3II2) visualized the full tertiary assembly, highlighting κ-ζ stabilization of DI and DVI docking.^[11] Subsequent cryo-EM structures of group IIA and IIB lariat introns at 3.5–3.8 Å resolution (PDB: 4R0D, 5G2X) captured η-η′ and γ-γ′ interactions in the post-branching state, revealing how Mg²⁺ sites at JII/III maintain core integrity.^[10] More recent work, including 2020 crystal structures of splicing mutants at 3.2–3.6 Å resolution (PDB: 6T3K, 6T3R), has illuminated protonation-driven toggling of the catalytic site between splicing steps, while cryo-EM structures of pre-catalytic ribonucleoprotein complexes at ~5 Å resolution (PDB: 7D0G) have revealed exon and maturase protein positioning prior to splicing.^[4]^[13] Folding proceeds hierarchically, with DI assembling first to provide a platform for other domains, followed by conformational changes in DVI that enable lariat formation. DVI undergoes a 90° swing or toggle between active (one-nucleotide bulge for branching) and silent (two-nucleotide bulge for ligation) states, stabilized by η-η′ docking and interactions with DI's J2/3 junction.^[10] This dynamic repositioning, observed in crystal structures of splicing intermediates, ensures sequential activation of the catalytic site without disrupting the overall fold.^[12]

Splicing Mechanism

Self-Splicing Pathway

Group II introns undergo self-splicing through a two-step transesterification mechanism that excises the intron and ligates the flanking exons. In the first step, the 2'-OH group of a bulged adenosine residue in domain VI (the branch point) performs a nucleophilic attack on the 5' splice site phosphodiester bond, cleaving the 5' exon and forming a lariat intermediate where the intron's 5' end is joined to the branch point via a 2'-5' phosphodiester linkage. In the second step, the 3'-OH of the freed 5' exon attacks the 3' splice site, resulting in exon ligation and release of the excised lariat intron. This pathway mirrors the splicing mechanism of nuclear pre-mRNA introns but occurs autocatalytically without spliceosomal proteins. Efficient self-splicing of group II introns in vitro requires specific ionic and thermal conditions to promote RNA folding and catalysis. High concentrations of Mg²⁺ (typically around 100 mM) are essential to stabilize the ribozyme's tertiary structure and facilitate divalent metal ion coordination in the active site, while monovalent ions such as NH₄⁺ (around 500 mM) screen electrostatic repulsions and aid in domain assembly. Elevated temperatures, often 42–50°C, further enhance folding kinetics and reaction rates, though optimal conditions vary slightly among introns. In vivo, associated proteins like maturases promote efficient splicing under physiological conditions (e.g., ~1-5 mM Mg²⁺). These non-physiological in vitro requirements highlight the role of associated proteins in vivo for efficient splicing under cellular conditions. Unlike group I introns, which initiate splicing via an exogenous guanosine cofactor that attacks the 5' splice site to form a linear intermediate, group II introns use an internal branch point adenosine for the first transesterification, producing a characteristic lariat structure without external cofactors. This distinction underscores the evolutionary divergence between the two ribozyme classes, despite shared reliance on two transesterification steps for splicing. The self-splicing pathway was first demonstrated experimentally using the ai5γ group IIB intron from the yeast Saccharomyces cerevisiae mitochondrial COX1 gene, where in vitro transcription of precursor RNA led to accurate excision of the lariat intron and exon ligation under high-Mg²⁺ conditions. Subsequent studies with ai5γ confirmed the branch point role of the conserved adenosine in domain VI through mutagenesis and mapping of the lariat structure. These in vitro systems provided foundational evidence for the ribozyme's autocatalytic nature and have been instrumental in elucidating the mechanism across group II introns.

Catalytic Mechanism

The catalytic mechanism of group II introns operates through a ribozyme-mediated general acid-base catalysis, primarily orchestrated by the conserved AGC triad located at the 5' end of domain V (DV). This triad, consisting of adenine, guanine, and cytosine nucleotides (or CGC in some group IIC introns), forms a catalytic triplex with nucleotides from the J2/3 linker, positioning the branch-point adenosine and the scissile phosphate for nucleophilic attack while coordinating essential metal cofactors. The AGC triad coordinates metal ions to facilitate phosphoryl transfer during both transesterification steps.^[14] Central to this chemistry is the two-metal-ion mechanism for phosphoryl transfer, involving two Mg²⁺ ions (M1 and M2) at the active site, a paradigm inspired by studies on RNase P ribozyme. M1 activates the 2'-hydroxyl nucleophile of the branch-point adenosine by polarizing it for inline attack on the 5' splice site phosphate, while M2 stabilizes the developing negative charge on the pentacoordinate transition state and aids in leaving group departure; the ions are typically separated by ~3.9–4 Å and coordinated by non-bridging phosphate oxygens and DV residues.^[15] A distinct second divalent metal ion is required specifically for the exon-ligation step, where it activates the 3'-hydroxyl of the upstream exon for attack on the branch-point phosphate, ensuring efficient second-step chemistry without cyclic intermediates.^[16] This mechanism underlies the two sequential transesterification reactions of self-splicing. The reaction's efficiency is highly sensitive to pH and ionic conditions, which modulate active site protonation and metal binding. The branching step rate shows pH dependence, with protonation of catalytic elements influencing nucleophile activation. Optimal catalysis requires 5–10 mM Mg²⁺ for metal ion coordination and 100–500 mM monovalent cations (e.g., K⁺ or NH₄⁺) to stabilize the ribozyme core, with Na⁺ or high ionic strength inhibiting by disrupting domain interactions.^[12] Under standard in vitro conditions (pH 7.5, 5 mM Mg²⁺, 150 mM K⁺, 37–45°C), representative k_br values range from 0.14 min⁻¹ for the ai5γ intron to 0.75 min⁻¹ for the faster I3 intron, while the exon ligation step (k_2nd) proceeds at comparable rates (~0.1–0.5 min⁻¹), often limited by conformational toggling between steps.^[17] Recent cryo-EM structures (2023–2025) of group IIC introns and other variants, including high-resolution ribonucleoprotein complexes and ensemble refinements, have illuminated a heteronuclear active site core comprising two Mg²⁺ ions and two K⁺ ions, which precisely positions the branch-point adenosine's 2'-OH for attack at 2.3 Å from the scissile phosphate, confirming the two-metal-ion model's role in both splicing steps and highlighting dynamic domain VI repositioning without core disassembly. These findings extend to broader RNA catalysis by demonstrating how metal clusters enable precise nucleophile activation in large ribozymes, informing computational models of metal-dependent RNA catalysis as of 2025.^[18]^[19]^[20]

Associated Proteins

Maturase Function

Maturases are intron-encoded proteins (IEPs) that function as splicing factors specific to group II introns, originating from open reading frames (ORFs) typically located in domain IV of the intron RNA.^[21] These proteins evolved from reverse transcriptase ancestors associated with mobile genetic elements, adapting to promote RNA splicing in addition to their role in intron mobility.^[21] By stabilizing the intron's secondary and tertiary structures, maturases enhance splicing efficiency, particularly in vivo where self-splicing alone is often inefficient due to suboptimal ionic conditions or RNA misfolding.^[22] Maturases bind primarily to domain IV (DIV), forming a high-affinity interaction that nucleates proper RNA folding, with additional contacts to the catalytic core domains (DI, DII, DV, and DVI) to promote tertiary interactions essential for catalysis.^[22] The binding to DIVa, for instance, occurs with picomolar affinity (K_d ≈ 0.25 pM), positioning the protein to chaperone conformational changes that align active site residues.^[22] These interactions lower the magnesium ion concentration required for splicing and stabilize otherwise transient RNA structures, thereby accelerating the reaction rate.^[21] A well-studied example is the maturase from the Lactococcus lactis Ll.LtrB intron (LtrA protein), which binds its cognate RNA as a monomer and boosts splicing efficiency by 10- to 100-fold, depending on conditions such as magnesium levels (e.g., ~25-fold at 50 mM Mg²⁺).^[21] LtrA's reverse transcriptase domain contributes to DIV binding via the RT0 motif, while its X domain interacts with DI to further stabilize the active conformation.^[22] This targeted enhancement contrasts with general host factors in organelles, which assist multiple introns non-specifically; maturases, by contrast, are highly intron-specific, recognizing unique sequence and structural features of their parent intron to ensure precise splicing.^[21]

Reverse Transcriptase Domain

The reverse transcriptase (RT) open reading frame (ORF) of group II introns is inserted within domain IV (DIV) of the intron RNA, forming a characteristic loop structure that allows the encoded protein to bind and stabilize the intron during splicing and mobility.^[23] This ORF encodes a multifunctional intron-encoded protein (IEP) with an N-terminal RT domain responsible for synthesizing cDNA during retrohoming, the intron-encoded mobility process. The RT domain features seven conserved motifs (RT0–RT7), which are critical for DNA polymerization and are analogous to those in retroviral RTs; these include the RT0 loop in the N-terminal extension (NTE), RT1–RT7 in the fingers and palm subdomains, and insertions like RT2a and RT3a that enhance template handling.^[24] The overall architecture comprises thumb, fingers, and palm subdomains, with the thumb providing processivity through interactions with the template-primer duplex.^[23] Group II intron RTs share an evolutionary origin with non-long terminal repeat (non-LTR) retrotransposons, such as human LINE-1 elements, reflecting a common ancestry among bacterial, organellar, and eukaryotic mobile elements that propagate via target-primed reverse transcription.^[25] This relatedness is evident in the conserved RT core, including the NTE/RT0, RT2a, RT3a insertions, and an extended thumb subdomain, which facilitate accurate cDNA synthesis from highly structured RNA templates.^[5] Unlike retroviral RTs, group II intron RTs exhibit adaptations for high-fidelity replication, minimizing errors during intron propagation.^[25] Biochemical characterization of group II intron RTs, often achieved by expressing the proteins in Escherichia coli as fusion constructs for purification, reveals robust polymerase activity with superior processivity and fidelity compared to many viral RTs. For instance, thermostable variants like TeI4c RT and GsI-IIC RT synthesize full-length cDNAs averaging 700–714 nucleotides at elevated temperatures (up to 60–81°C), far exceeding the ~176 nucleotides of SuperScript III RT under similar conditions.^[26] Fidelity assays using M13-based lacZ forward mutation detection yield error rates of 0.64–0.86 × 10⁻⁵ errors per base pair, outperforming SuperScript III's 1.5 × 10⁻⁵, which supports their role in precise retrohoming without sequence degradation.^[26] These properties stem from structural features like the RT3a insertion, which modulates active site access, and the thumb's stabilizing interactions.^[5] A 2025 structural study of a domesticated group II intron-like RT (G2L4 RT) provides insights into its evolution for host DNA repair functions, such as microhomology-mediated end-joining at double-strand breaks, while retaining core RT features for potential biotechnological optimization. Crystal structures (2.6–2.8 Å resolution) reveal a homodimeric enzyme with conserved RT motifs and a unique RT3a "plug" that autoinhibits the active site via salt bridges and hydrophobic contacts, which can be engineered for enhanced activity in genome editing applications.^[5] The NTE/RT0 loop, enriched in serines, promotes strand annealing at short microhomologies (2–5 nt), suggesting targeted modifications to the dimer interface and active site (e.g., YxDD motif) could improve fidelity and processivity for synthetic biology tools.^[5]

Mobility and Retrohoming

Intron Invasion Process

The retrohoming of group II introns occurs through a target-primed reverse transcription (TPRT) mechanism, a copy-and-paste process that enables the intron to insert itself into a new DNA site without excising from its original location. In this pathway, the excised intron RNA, complexed with its multifunctional protein encoded by the intron (IEP), forms a ribonucleoprotein (RNP) particle that recognizes and invades a homologous target DNA sequence. The TPRT model involves the intron RNA reverse-splicing directly into a nick in the target DNA, followed by reverse transcription to synthesize a cDNA copy, and completion of integration via second-strand DNA synthesis.^[27] The process initiates with site-specific cleavage of the target DNA by the endonuclease activity of the IEP's reverse transcriptase (RT) domain, which contains a homing endonuclease subdomain (often called the En or X domain) essential for generating a single-strand nick approximately 9-11 nucleotides downstream of the insertion site in the target DNA's 3' exon. This nick serves as the primer for reverse splicing, where the 3' end of the intron RNA attacks the cleaved DNA strand, inserting the intron via a transesterification reaction analogous but reverse to forward splicing. Subsequently, the RT domain extends from the 3' end of the inserted RNA, using it as a template to synthesize the cDNA, which displaces the downstream target DNA strand. The efficiency of retrohoming is highly dependent on the homing endonuclease domain, as mutations or absence of this domain significantly reduce cleavage and insertion rates, often dropping mobility to less than 1% of wild-type levels in model systems like the Lactococcus lactis Ll.LtrB intron.^[28]^[29] Final integration requires host DNA repair machinery to synthesize the second strand and resolve the displaced flap of target DNA, often resulting in short direct repeats flanking the inserted intron. Cryo-EM structures resolved in 2019 at 3.6 Å resolution captured key intermediates of the reverse splicing step for the bacterial Thermosynechococcus elongatus group II intron, revealing how domain VI of the intron RNA coordinates magnesium ions and interacts with the target DNA nick to facilitate branch-point formation and strand invasion.^[30] These structures highlight the dynamic conformational changes in the RNP complex during TPRT, providing atomic-level insights into the mechanism's fidelity and specificity. A 2022 cryo-EM study of a group IIC intron RNP further visualized the complex poised for DNA attack, showing minimal conformational changes and molecular recognition strategies without major rearrangements.^[31] Subsequent studies have built on these findings, confirming the model's applicability across bacterial and organellar group II introns.

Target Recognition and Integration

Group II introns recognize their genomic target sites primarily through base-pairing interactions between exon-binding sites (EBS) in the intron RNA and complementary intron-binding sites (IBS) in the target DNA, mirroring the RNA-RNA pairings used during splicing. This system ensures site-specific integration, with EBS2 in domain I of the intron RNA pairing with IBS2 in the 5' exon of the target, typically forming a 5-6 base-pair helix that contributes to initial binding stability.^[32] In group IIA introns, such as Ll.LtrB from Lactococcus lactis, this is complemented by EBS1-IBS1 (6-8 nt) and a short δ-δ' interaction (2 nt), spanning a core 13-nucleotide recognition region from positions -12 to +1 relative to the insertion site.^[32] Recent studies have identified an additional EBS2a-IBS2a pairing adjacent to EBS2-IBS2, which stabilizes the complex by inducing a loop structure that prevents dissociation.^[33] The intron-encoded protein (IEP) enhances specificity through its endonuclease domain, which cleaves the antisense strand of the target DNA. In Ll.LtrB, cleavage occurs at position +9 in the 3' exon, approximately 9 nucleotides downstream of IBS1, generating a 3' overhang that primes reverse transcription during integration.^[32] Spacer lengths between IBS elements are tightly constrained; for instance, a 4-6 nucleotide spacer separates IBS1 and IBS2, and deviations of even 1-2 nucleotides abolish activity by disrupting helical geometry.^[23] Variable spacers upstream of IBS2 (up to 20-30 nt) allow flexibility in target selection, but the IEP recognizes flanking sequences (e.g., -21 to -11) via direct readout, ensuring precise positioning.^[34] Integration exhibits high fidelity, with retrohoming efficiency reaching nearly 100% at cognate sites in vitro, though error rates increase with mismatches in EBS/IBS pairings. Single nucleotide substitutions in critical IBS positions (e.g., -10 or +1) can reduce activity by over 100-fold, reflecting redundant protein-RNA interactions that enforce specificity.^[32] Off-target effects are minimal in bacterial systems like Ll.LtrB, with ectopic integration rates of 0.1-30 × 10^{-6} in E. coli, often limited to sites with partial IBS complementarity.^[23] In contrast, organellar group II introns, which frequently lack a functional endonuclease domain, show higher variability and lower overall mobility, relying more heavily on RNA pairing alone and resulting in sporadic off-target insertions during mitochondrial or chloroplast genome evolution.^[35] A representative example is the Ll.LtrB intron's targeting of the ltrB gene in Lactococcus lactis, where conserved motifs in the IBS include a G at position -21 (facilitating reverse splicing) and a T at +5 (essential for antisense cleavage). Sequence analyses reveal strong conservation in IBS1 (e.g., 5'-TCTGA-3' core) and IBS2 (e.g., 5'-GTTA-3'), as depicted in consensus logos from mutagenesis studies, underscoring the modular nature of recognition that enables retargeting for biotechnological applications.^[32]

Distribution and Evolution

Occurrence in Genomes

Group II introns are widely distributed in bacterial genomes, with notable abundance in the phyla Firmicutes and Actinobacteria, where they account for a substantial fraction of identified introns across sequenced species.^[36] In these lineages, introns often insert into essential genes, including those within rRNA operons, potentially influencing ribosomal function while relying on self-splicing mechanisms for viability.^[37] Overall, group II introns occur in approximately 25% of analyzed bacterial genomes, averaging about five per genome, though their density varies by phylum, with higher concentrations in Firmicutes reflecting historical proliferation events.^[37] In eukaryotic organelles, group II introns are highly prevalent in the mitochondria and chloroplasts of plants and fungi, where hundreds have been cataloged across diverse species, contributing significantly to non-coding sequences.^[38] For instance, land plant mitochondrial genomes contain variable numbers of these introns, often exceeding 20 per genome in angiosperms, while chloroplasts maintain around 22 positionally conserved group II introns.^[38] In contrast, animal mitochondria harbor far fewer group II introns, with most metazoan lineages showing complete absence or only sporadic occurrences in basal groups like sponges.^[39] Recent analyses employing covariance models for RNA structure detection have uncovered group II introns in bacteriophage genomes, indicating their infiltration into viral elements across diverse phage types, from endosymbiont-associated to jumbo phages.^[40] This finding, reported in 2025 studies, broadens the ecological scope of these mobile elements beyond cellular hosts.^[41] Group II introns exhibit subgroup variations in distribution: subgroup IIA predominates in bacterial genomes, often associated with active retrohoming; IIB is characteristic of organellar genomes in plants and fungi; and IIC appears in diverse prokaryotic lineages, including both bacteria and archaea.^[35]

Phylogenetic Analysis

Group II introns are classified into three major subgroups—IIA, IIB, and IIC—primarily based on variations in the secondary structures of domains I (DI) and II (DII), which influence their splicing efficiency and mobility. Subgroup IIA introns feature a distinct DI structure with an additional stem-loop in DII, while IIB introns exhibit a more variable DI lacking that stem-loop but with diverse insertions in DII, making IIB the most diverse and widespread subgroup, particularly in bacterial genomes. In contrast, IIC introns have a simplified DI and are typically smaller, often lacking an intron-encoded protein (IEP). This classification, established through comparative structural analysis, highlights how structural divergences correlate with functional adaptations across diverse hosts.^[42] Phylogenetic analyses of group II introns rely on sequences from either the reverse transcriptase (RT) domains of IEPs or the conserved RNA core regions, revealing a monophyletic origin in bacteria followed by multiple transfers to organelles. Trees constructed from RT amino acid sequences (e.g., using maximum likelihood methods on ~400 aligned positions) show well-supported clades corresponding to the IIA, IIB, and IIC subgroups, with bacterial lineages forming the basal branches and organellar introns nesting within them, indicative of endosymbiotic transfers from alphaproteobacterial and cyanobacterial ancestors to mitochondria and plastids, respectively. RNA core phylogenies (based on ~140 nucleotides in domains V and VI) largely mirror RT trees but exhibit some conflicts, suggesting occasional RNA structure evolution independent of the protein component. These analyses underscore the ancient bacterial roots of group II introns, with diversification driven by retrohoming mechanisms.^[42]^[43] Evidence for horizontal gene transfer (HGT) is prominent in group II intron evolution, as their phylogenetic distributions often incongrue with host organism phylogenies. For instance, closely related IIB introns appear in distantly related bacterial genera, such as Pseudomonas and Bacillus, implying interspecies mobility via retrohoming or conjugation-like processes. In organellar contexts, HGT is exemplified by the transfer of a group IIB intron from a cyanobacterial donor to the Euglena chloroplast genome, where the intron's phylogeny aligns more closely with free-living cyanobacteria than with the algal host lineage, supporting ancient invasions during plastid endosymbiosis. Such incongruences highlight HGT as a key driver of intron dissemination beyond vertical inheritance.^[43]^[44] Recent studies from 2024 and 2025 have advanced understanding of splicing factor evolution in land plants, revealing how nuclear-encoded proteins compensate for the degeneration and loss patterns of mitochondrial group II introns. In land plant mitochondria, most introns have lost their IEPs and self-splicing capability, leading to reliance on diverse cofactors like pentatricopeptide repeat (PPR) proteins and maturases, which have co-evolved to recognize degenerate RNA structures. For example, the 2024 review details how intron loss via precise excision or reverse transcription correlates with the expansion of splicing factors such as RNA helicases (e.g., ZmRH48), enabling efficient processing despite structural erosion. Similarly, the 2025 discovery of plant organelle RNA recognition (PORR) proteins demonstrates their role in binding specific intron regions to facilitate trans-splicing, linking the evolutionary shift toward protein-assisted mechanisms to patterns of intron retention and loss in angiosperms. These findings illustrate ongoing adaptation in plant organelle genomes, where splicing factor diversification mitigates the impacts of intron degeneration.^[45]

Biological Roles and Applications

Evolutionary Significance

Group II introns, originating from bacterial ancestors, played a pivotal role in eukaryotic evolution by entering the proto-eukaryotic cell through the α-proteobacterial endosymbiont that became the mitochondrion. These mobile elements proliferated within the emerging nuclear genome, where their self-splicing machinery evolved into the core components of the spliceosome, including small nuclear RNAs U2, U5, and U6, as well as the essential protein Prp8.^[5] This transition is evidenced by the structural and functional similarities between group II intron ribozymes and spliceosomal introns, which arose during the prokaryote-to-eukaryote shift, with the last eukaryotic common ancestor (LECA) exhibiting high intron density comparable to modern spliceosomal systems.^[46]^[2] The mobility of group II introns facilitated their invasion and subsequent loss or retention in organelle genomes, significantly influencing compaction and stability. In bacterial hosts, these introns actively retrohome via target-primed reverse transcription (TPRT), but in mitochondria and chloroplasts, mobility diminished, leading to widespread intron degeneration or elimination, which streamlined organelle genomes by reducing non-coding sequences.^[2] For instance, many organellar introns lost their intron-encoded proteins (IEPs), becoming dependent on host factors and contributing to the compact architecture observed in plant and algal organelles.^[2] Group II introns exhibit striking parallels to eukaryotic retrotransposons, particularly LINE elements, positioning them as evolutionary progenitors through shared TPRT mechanisms. Both utilize an endonuclease to nick target DNA, priming reverse transcription of an RNA intermediate to insert copies, a process conserved from ancient bacterial introns to modern non-LTR retrotransposons like human LINE-1.^[47]^[48] This homology underscores group II introns' influence on genome plasticity across domains of life. Recent 2025 analyses reinforce mobile group II introns' central role in eukaryogenesis, highlighting mechanisms like RNA circularization that enhance their persistence in early eukaryotic lineages. Natural circularly permuted variants in bacteria generate stable circular RNAs via self-splicing, potentially aiding intron survival during endosymbiotic integration and nuclear proliferation.^[5]^[49]

Biotechnological and Research Uses

Group II introns have emerged as versatile tools for gene targeting due to their site-specific retrohoming mechanism, particularly the Ll.LtrB intron from Lactococcus lactis, which enables precise DNA integration in diverse organisms.^[50] In bacteria, reprogrammed Ll.LtrB introns facilitate targeted gene insertions and disruptions by recognizing specific DNA sequences via guide RNAs, allowing efficient chromosomal modifications without off-target effects.^[50] This approach has been extended to eukaryotes, where Ll.LtrB-mediated retrohoming achieves stable integration into yeast and plant genomes, supporting applications in metabolic engineering and trait improvement.^[51] In mammalian cells, engineered Ll.LtrB ribonucleoprotein complexes localize to the nucleus and catalyze intron insertion at predefined sites, demonstrating up to 10% efficiency in human cell lines and paving the way for non-viral gene therapy vectors.^[52] Recent advancements in genome engineering leverage domesticated variants of group II intron reverse transcriptases (RTs) to enhance fidelity and utility.^[53] Structural studies in 2025 revealed adaptations in these RTs for host DNA repair functions, with substitutions at the active site potentially trading higher fidelity for enhanced repair efficiency.^[54] Engineered introns incorporating these optimized RTs enable scarless genome editing in bacterial and eukaryotic systems, outperforming traditional recombinases in specificity for large payload delivery.^[53] Group II introns also support RNA circularization for therapeutic applications, exploiting their self-splicing activity to generate stable circular RNAs (circRNAs).^[55] In 2025, in vitro systems using intact group II introns demonstrated efficient circularization of exogenous RNAs via trans-splicing, yielding circRNAs with half-lives exceeding 48 hours in cellular environments, enhancing protein expression for vaccine and gene therapy platforms.^[55] These self-splicing mechanisms, adapted from group IIC introns, produced circular RNA vaccines eliciting robust immune responses in preclinical models, with circularization efficiencies reaching 80% without enzymatic scars.^[56] In research, group II introns serve as models for ribozyme studies through in vitro splicing assays that dissect catalytic mechanisms and cofactor requirements.^[50] These assays, using purified intron RNAs, quantify splicing kinetics under varying ionic conditions, informing designs for synthetic ribozymes in nanotechnology.^[50] In plant biology, 2025 investigations highlighted the role of pentatricopeptide repeat (PPR)-related PORR proteins in facilitating group II intron splicing within mitochondrial genomes, binding specific intron regions to facilitate trans-splicing in Arabidopsis models.^[57] This advance elucidates organelle gene expression regulation and aids in engineering mitochondrial traits for crop resilience.^[58]

References

[1]
Group II Introns: Flexibility and Repurposing - Frontiers
Group II introns are extraordinarily versatile self-splicing ribozymes and retrotransposable elements widespread in bacteria and in bacterial-derived organelles ...
[2]
Evolution of group II introns - PMC - PubMed Central
The 2- to 3-kb sequence consists of RNA and protein portions. The intron RNA domains are depicted in red and demarcated with Roman numerals.
[3]
Visualizing group II intron dynamics between the first and second ...
Jun 5, 2020 · Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the ...
[4]
https://www.nature.com/articles/s41467-020-16741-4
[5]
https://www.pnas.org/doi/10.1073/pnas.2504208122
[6]
https://doi.org/10.1016/s0300-9084(82)80038-4
[7]
The tertiary structure of group II introns: implications for biological ...
Group II introns are some of the largest ribozymes in nature, and they are a major source of information about RNA assembly and tertiary structural ...
[8]
Structural insights into the mechanism of group II intron splicing - PMC
Jun 1, 2018 · These studies expand our understanding of group II intron structural diversity and evolution, while setting the stage for rigorous mechanistic analysis of RNA ...Missing: zeta | Show results with:zeta
[9]
Visualizing the ai5γ group IIB intron | Nucleic Acids Research
Here, we modeled the molecular structure of the ai5γ group IIB intron from yeast using the crystal structure of a bacterial group IIC homolog.
[10]
https://pmc.ncbi.nlm.nih.gov/articles/PMC5492998/
[11]
https://academic.oup.com/nar/article/42/3/1947/1056107
[12]
https://www.cell.com/cell/fulltext/S0092-8674(12)01179-8
[13]
https://academic.oup.com/nar/article/48/19/11185/5918319
[14]
https://doi.org/10.1016/j.bbagrm.2019.06.001
[15]
https://doi.org/10.1016/j.molcel.2006.03.013
[16]
https://doi.org/10.1016/j.chembiol.2007.05.008
[17]
https://doi.org/10.1093/emboj/20.23.6866
[18]
Biotechnological applications of mobile group II introns and their ...
Jan 13, 2014 · Group II intron RTs contain conserved N-terminal RT and X domains, which correspond to the fingers/palm and thumb domains of retroviral RTs, ...
[19]
Domain structure and three-dimensional model of a group II intron ...
Dec 1, 2004 · LtrB group II intron contains an N-terminal RT domain, with conserved sequence motifs RT1 to 7 found in the fingers and palm of retroviral RTs; ...
[20]
Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution
DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, ...
[21]
Structural basis for the evolution of a domesticated group II intron ...
Jul 29, 2025 · The structures provide insights into how an RT can function in DNA repair and suggest ways of optimizing RTs for genome engineering applications ...
[22]
Thermostable group II intron reverse transcriptase fusion proteins ...
This paper describes unusual properties of group II intron-encoded reverse transcriptases. They have higher processivity, fidelity, and thermostability than ...
[23]
Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution
In group II introns, the catalytic Mg2+ ions bind to DV via a CGC triad and bulge, whereas U6 contains an AGC triad and bulge that position the catalytic Mg2+ ( ...
[24]
Bacterial group II introns: not just splicing - Oxford Academic
This review summarizes what is known about the splicing mechanisms and mobility of bacterial group II introns, and describes the recent development of group II ...
[25]
Evolution of group II introns | Mobile DNA | Full Text - BioMed Central
Apr 1, 2015 · For example, the γ-γ′ interaction of group II introns is a Watson-Crick base pair between a J2/3 nucleotide and the last position of the intron ...Missing: kappa- zeta eta-
[26]
Retrotransposition of a yeast group II intron occurs by reverse ...
We show that the yeast mtDNA group II intron aI1 retrotransposes by reverse splicing directly into an ectopic DNA site.
[27]
Rules for DNA target-site recognition by a lactococcal group II intron ...
Abstract. Group II intron homing occurs primarily by a mechanism in which the intron RNA reverse splices into a DNA target site and is then reverse ...Results · Effect Of Gc Content And... · In Vivo Assays With Mutant...
[28]
new RNA–DNA interaction required for integration of group II intron ...
We demonstrate the existence of a new base-pairing interaction named EBS2a–IBS2a between the intron RNA and its DNA target site.
[29]
Group II intron endonucleases use both RNA and protein subunits ...
The IBS2 sequence in the DNA target site is recognized primarily by base pairing with the intron RNA. The situation for the IBS2/EBS2 interaction was more ...
[30]
Group II Introns: Mobile Ribozymes that Invade DNA - PubMed Central
Group II introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by ...
[31]
Group II introns in Eubacteria and Archaea: ORF-less introns ... - NIH
Overall, group II introns are found in six subdivisions of Eubacteria (Acidobacteria, Actinobacteria, Bacteroidetes/Chlorobi, Cyanobacteria, Firmicutes, and ...Missing: rRNA | Show results with:rRNA
[32]
Distinct Expansion of Group II Introns During Evolution of ... - Frontiers
Group II Introns With Specific Intron-Encoded Protein Types Tend to Integrate Just After Rho-Independent Transcription Terminators. We have shown that bacterial ...Missing: operons | Show results with:operons
[33]
Categorizing 161 plant (streptophyte) mitochondrial group II introns ...
Mar 13, 2023 · Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly ...
[34]
Mitochondrial group I and group II introns in the sponge orders ...
Dec 12, 2015 · Within mitochondrial genomes, Group I introns are preponderant in fungi, Group II introns are predominant in plants [5], and both groups are ...
[35]
Presence of group II introns in phage genomes - PMC - NIH
Aug 13, 2025 · Advances in RNA structure-based homology searches using covariance models has provided the ability to identify the conserved secondary ...
[36]
Prevalence of Group II Introns in Phage Genomes - bioRxiv
May 23, 2025 · We discover that group II introns are widely prevalent in phages from diverse phylogenetic backgrounds, from endosymbiont phage to jumbophage.
[37]
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.849080/full
[38]
Phylogenetic relationships among group II intron ORFs - PMC - NIH
Group II introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history.Missing: classification ABC
[39]
Recent horizontal intron transfer to a chloroplast genome - PMC
Evidence is presented for the recent, horizontal transfer of a self-splicing, homing group II intron from a cyanobacteria to the chloroplast genome of Euglena ...Missing: incongruence | Show results with:incongruence
[40]
https://pmc.ncbi.nlm.nih.gov/articles/PMC12350094/
[41]
The spread of the first introns in proto-eukaryotic paralogs - Nature
May 19, 2022 · It has been established that spliceosomal introns originated from prokaryotic self-splicing group II introns during the prokaryote-to-eukaryote ...
[42]
Telomerase and retrotransposons: Reverse transcriptases ... - PNAS
Dec 20, 2011 · Retrotransposition of a TP retrotransposon or group II intron is usually initiated by endonucleolytic cleavage, exposing a 3′-OH that serves as ...
[43]
Structures, functions and adaptations of the human LINE-1 ORF2 ...
Dec 14, 2023 · ... group II introns again closest to ORF2p. Group IIB introns are thought to be evolutionarily closer to L1 than group IIC, but intriguingly ...
[44]
Natural circularly permuted group II introns in bacteria produce RNA ...
Dec 17, 2021 · The Ll.LtrB intron from Lactococcus lactis excises as circles in vivo: insights into the group II intron circularization pathway. RNA, 21 ...
[45]
Biotechnological applications of mobile group II introns and their ...
Jan 13, 2014 · Mobile group II introns are bacterial retrotransposons that perform a remarkable ribozyme-based, site-specific DNA integration reaction (' ...
[46]
Retrohoming of a Mobile Group II Intron in Human Cells Suggests ...
Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ...
[47]
Localization of a bacterial group II intron-encoded protein in human ...
Aug 5, 2015 · Most bacterial group II introns have a multifunctional intron-encoded protein (IEP) ORF within DIV2. ... Group II introns have high insertion ...
[48]
Structural basis for the evolution of a domesticated group II intron ...
Jul 29, 2025 · Our findings reveal how an RT can function in DNA repair and suggest ways of optimizing related RTs for genome engineering applications. Reverse ...
[49]
Structural basis for the evolution of a domesticated group II intron ...
Our findings reveal how an RT can function in DNA repair and suggest ways of optimizing related RTs for genome engineering applications. Keywords: DNA ...
[50]
Self-splicing RNA circularization facilitated by intact group I and II ...
Aug 10, 2025 · Effective circularization via self-splicing introns relied on ribozyme activity, requiring optimal Mg2+ concentration, temperature, and reaction ...
[51]
Group IIC self-splicing intron-derived novel circular RNA vaccine ...
Apr 10, 2025 · Methods: Here, we demonstrate that group IIC self-splicing introns can efficiently circularize and express exogenous proteins of varying lengths ...
[52]
Plant mitochondrial PORR proteins facilitate group II intron splicing ...
Aug 18, 2025 · Unlike their autocatalytic progenitor, plant mitochondrial introns are highly degenerate and have lost the capacity of self-splicing. Many ...
[53]
Plant mitochondrial PORR proteins facilitate group II intron splicing ...
Aug 11, 2025 · Plant mitochondrial PORR proteins facilitate group II intron splicing by binding to distinct regions within their target introns ... mitochondrial ...Missing: assays ribozyme models advances