Glossary

C

• Class I Elements: Class I elements, also known as Class I transposable elements or retrotransposons, are a type of mobile genetic element found in the genomes of various organisms, including humans. They are characterized by their mode of transposition, which involves an RNA intermediate. The process of transposition for Class I elements involves several steps:
  1. Transcription: The Class I element is transcribed into an RNA molecule.
  2. Reverse transcription: A reverse transcriptase enzyme, typically encoded by the element itself, converts the RNA molecule into complementary DNA (cDNA).
  3. Integration: The cDNA is integrated into a new location within the genome, either directly or via a DNA intermediate. Class I elements can be further divided into several subclasses based on their structure and mechanism of transposition:
  4. Long Terminal Repeat (LTR) retrotransposons: These elements contain long terminal repeat sequences at their ends and are structurally similar to retroviruses. They transpose via a virus-like particle and use an integrase enzyme for integration.
  5. Non-LTR retrotransposons: These elements lack the LTR sequences and can be further divided into two main groups: long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). LINEs encode the proteins required for their own transposition, while SINEs rely on the proteins encoded by LINEs for their mobility.
  6. Penelope-like elements (PLEs): These are a less common type of retrotransposon found primarily in eukaryotes. They are characterized by their unique structure and reverse transcriptase. Class I elements can have significant impacts on the structure and function of genomes, as their transposition can lead to insertions, deletions, duplications, and rearrangements. While they can sometimes be harmful to the host organism, they can also contribute to genomic diversity and evolution (see also).
• Class II Elements: Class II elements, also known as Class II transposable elements or DNA transposons, are a type of mobile genetic element found in the genomes of various organisms. Unlike Class I elements, which transpose through an RNA intermediate, Class II elements move within the genome directly through a DNA-based mechanism. The transposition of Class II elements typically involves the following steps:
  1. Excision: The Class II element is excised from its original position in the genome. This process is usually mediated by a transposase enzyme, which is encoded by the transposable element itself.
  2. Integration: The excised Class II element is inserted into a new location within the genome. The transposase enzyme typically recognizes specific target sites, called terminal inverted repeats (TIRs), at the ends of the transposon, as well as a short sequence at the target site. Class II elements can be further divided into several subclasses based on their structure and mechanism of transposition:
  3. Cut-and-paste transposons: These are the most common type of Class II elements. They are characterized by their TIRs and move through a cut-and-paste mechanism, which involves the excision of the element from one location and its integration into a new location.
  4. Rolling-circle transposons: Also known as Helitrons, these elements transpose through a rolling-circle mechanism, where the transposon is replicated and inserted into a new location without excising the original copy.
  5. Composite transposons: These elements consist of two insertion sequences (IS elements) that flank a central region containing one or more genes. They can transpose as a single unit when the transposase enzyme recognizes and acts on the flanking IS elements. Like Class I elements, Class II elements can impact the structure and function of genomes through insertions, deletions, duplications, and rearrangements. They can be both beneficial and harmful to the host organism, contributing to genomic diversity, evolution, and occasionally causing genetic diseases (see also)
• Cre Recombinase: Cre recombinase is an enzyme derived from the bacteriophage P1, a type of virus that infects bacteria. It is a site-specific DNA recombinase that belongs to the integrase family of enzymes. Cre recombinase recognizes specific DNA sequences called loxP sites, which are 34 base pairs long and consist of two 13-base pair inverted repeats separated by an 8-base pair spacer region. The primary function of Cre recombinase is to catalyze the recombination between two loxP sites present in a DNA molecule. Depending on the orientation and location of the loxP sites, Cre recombinase can mediate various DNA rearrangements, such as excision, inversion, or integration of the DNA segment flanked by the loxP sites. Cre recombinase has become a valuable molecular tool in genetics and molecular biology research, particularly in the study of gene function and regulation in eukaryotic organisms, including mice and other model organisms. The Cre-loxP system allows researchers to perform conditional and tissue-specific gene knockouts, which involve the deletion or inactivation of a specific gene in a spatially or temporally controlled manner. This approach provides more precise control over gene function and helps researchers study the roles of specific genes in development, physiology, and disease. Additionally, the Cre-loxP system can be used for lineage tracing, which involves marking and tracking the progeny of specific cell populations over time, as well as for the generation of transgenic organisms and the manipulation of large genomic segments (see also).
• Co-integrate: A co-integrate is a molecular intermediate formed during the transposition of some mobile genetic elements, particularly in the case of certain bacterial transposons. The co-integrate structure arises when two separate DNA molecules, each containing a copy of the mobile genetic element, become joined together through a recombination event involving the mobile element. Here's a simplified outline of the co-integrate formation process in the context of bacterial transposons:
  1. Excision: A transposase enzyme, encoded by the transposon, recognizes the terminal inverted repeats (TIRs) at the ends of the transposon and excises the element from its original location within the donor DNA molecule.
  2. Strand exchange: The transposase enzyme mediates a strand exchange between the ends of the excised transposon and a target site in the recipient DNA molecule. This process results in the formation of a co-integrate structure, where the donor and recipient DNA molecules are fused together, with the transposon connecting them.
  3. Resolution: The co-integrate can be resolved through a process called site-specific recombination, which is typically mediated by a resolvase enzyme. This event separates the co-integrate into two individual DNA molecules, each carrying a copy of the transposon. The co-integrate formation and resolution processes contribute to the replication and dissemination of mobile genetic elements within and between genomes, thereby playing a role in bacterial evolution and the spread of antibiotic resistance genes.
• Copy-and-paste transposition model: The copy-and-paste transposition model refers to a mechanism of transposable element mobility in which the transposable element is duplicated and the new copy is inserted into a different location within the genome. This process results in an increase in the number of copies of the transposable element. The copy-and-paste model is primarily associated with Class I transposable elements, also known as retrotransposons, which use an RNA intermediate during transposition. Here's a simplified outline of the copy-and-paste transposition process for retrotransposons:
  1. Transcription: The retrotransposon is transcribed into an RNA molecule.
  2. Reverse transcription: The RNA molecule is converted into complementary DNA (cDNA) by a reverse transcriptase enzyme, which is usually encoded by the retrotransposon itself.
  3. Integration: The cDNA molecule is inserted into a new location within the genome. This step is typically mediated by an integrase or endonuclease enzyme, which may also be encoded by the retrotransposon. The original copy of the retrotransposon remains in its initial location, while the new copy is inserted elsewhere, leading to an increase in the number of copies of the element within the genome. This mechanism allows retrotransposons to proliferate within the genome, potentially contributing to genomic diversity, evolution, and, in some cases, genetic instability or diseases. In bacteria, the copy-and-paste transposition model primarily applies to a specific subset of Class I transposable elements called bacterial insertion sequences (IS elements) that use the replicative transposition mechanism. IS elements are small, simple mobile genetic elements that typically consist of a transposase gene flanked by short terminal inverted repeats (TIRs). Replicative transposition in bacteria involves the following steps:
  4. Transcription and translation: The IS element is transcribed into RNA, which is then translated into the transposase protein.
  5. Formation of a synaptic complex: The transposase binds to the TIRs of the IS element and brings the two ends of the element together to form a synaptic complex.
  6. Cleavage and replication: The transposase cleaves one strand of the donor DNA at each end of the IS element, creating free 3' hydroxyl groups. The 3' hydroxyl groups then serve as primers for DNA replication, which generates a new copy of the IS element.
  7. Strand transfer: The newly synthesized IS element is inserted into the target DNA through a process called strand transfer, in which the target DNA is cleaved, and the IS element is ligated into the new location.
  8. Repair and ligation: The gaps in the target DNA and the donor DNA are repaired by cellular DNA repair machinery, and the IS element is ligated into the new location. As a result, the original IS element remains in its initial position, while the newly synthesized copy is inserted into a different location in the genome. This process allows IS elements to proliferate within the bacterial genome, contributing to genomic diversity and evolution. However, it can also cause genomic instability, disrupt genes, or promote the transfer of antibiotic resistance genes among bacteria. It is important to note that the copy-and-paste model is distinct from the cut-and-paste model associated with Class II transposable elements (DNA transposons), which involves the excision of the element from its original location and subsequent integration into a new location without duplication.
• Copy-out–Paste-in transposition model: see above (Copy-and-paste transposition model)
• Cut-and-paste transposition model: The cut-and-paste transposition model is a mechanism by which mobile genetic elements, primarily Class II transposable elements or DNA transposons, move within the genome. In this process, the transposable element is excised from its original location and integrated into a new location in the genome without duplicating itself. This model contrasts with the copy-and-paste transposition model, where the transposable element is duplicated, and a new copy is inserted into a different location. Here's a simplified outline of the cut-and-paste transposition process for DNA transposons:
  1. Transcription and translation: The DNA transposon is transcribed into RNA, which is then translated into the transposase protein, an enzyme responsible for the mobility of the transposon.
  2. Excision: The transposase binds to the terminal inverted repeats (TIRs) at the ends of the transposon and catalyzes the excision of the element from its original position in the genome. This process typically involves the formation of a hairpin structure at the ends of the transposon and staggered cuts in the target DNA, leaving short single-stranded overhangs.
  3. Integration: The excised transposon, still bound by the transposase, is inserted into a new location within the genome. The transposase mediates the strand transfer reaction, in which the ends of the transposon are ligated to the target DNA at the new location.
  4. Repair: The cellular DNA repair machinery fills in the single-stranded gaps at the site of integration and repairs the donor site from which the transposon was excised. This process typically results in the duplication of a short target site sequence flanking the integrated transposon. The cut-and-paste transposition model enables DNA transposons to move within the genome, contributing to genomic diversity, evolution, and, in some cases, genetic instability or diseases. However, unlike the copy-and-paste model, the cut-and-paste mechanism does not increase the number of transposon copies in the genome.

D

• Direct Repeats (DRs): In the context of transposable elements, direct repeats (DRs) are short DNA sequences that flank the mobile genetic element and are created as a consequence of the transposition process. These direct repeats are not part of the transposable element itself, but rather are a result of the integration mechanism. Direct repeats are generated during the integration of both Class I (retrotransposons) and Class II (DNA transposons) transposable elements:
  1. Class I transposable elements (retrotransposons): When a retrotransposon is reverse-transcribed and integrated into a new location in the genome, the target DNA is cleaved in a staggered manner, leaving short single-stranded overhangs. After the integration, the cellular DNA repair machinery fills in the gaps and ligates the DNA. This process results in the duplication of the target site sequence on either side of the integrated retrotransposon, creating direct repeats.
  2. Class II transposable elements (DNA transposons): During the cut-and-paste transposition process, the transposase enzyme binds to the terminal inverted repeats (TIRs) at the ends of the DNA transposon and catalyzes the excision and subsequent integration of the element into a new location. The target DNA is also cleaved in a staggered manner, and the transposon is ligated into the new site. The gaps left by the integration are filled by the cellular DNA repair machinery, resulting in the duplication of the target site sequence and the formation of direct repeats flanking the integrated transposon. These direct repeats are important for several reasons:
  3. They are a signature of the transposition event and indicate the presence of a transposable element in the genome.
  4. They may facilitate the excision of the transposable element during future transposition events, as some transposases can recognize and bind to direct repeats, enabling the enzyme to excise the element from its current location.
  5. Direct repeats can mediate genomic rearrangements, such as deletions, duplications, or inversions, if recombination occurs between the direct repeats flanking two different transposable elements. It is essential to distinguish direct repeats from the terminal inverted repeats (TIRs) that are part of the transposable element itself. While TIRs are found at both ends of DNA transposons and are recognized by the transposase enzyme, direct repeats are a result of the integration process and are found outside the transposable element in the flanking genomic DNA.
• DDE Domain: The DDE domain is a highly conserved catalytic domain found in the transposase enzymes of many Class II transposable elements, also known as DNA transposons. The DDE domain is named after the three conserved acidic amino acid residues (typically Aspartate-Aspartate-Glutamate or D-D-E) that are crucial for its function. These residues coordinate divalent metal ions, usually magnesium or manganese, which are essential for the catalytic activity of the transposase enzyme. Transposases with a DDE domain are responsible for the mobility of DNA transposons through the cut-and-paste mechanism. During transposition, the DDE domain mediates the following steps:
  1. Recognition and binding: The transposase, containing the DDE domain, recognizes and binds to the terminal inverted repeats (TIRs) at the ends of the DNA transposon.
  2. Excision: The DDE domain catalyzes the cleavage of the phosphodiester bonds at both ends of the transposon, releasing it from its original location in the genome. This process is facilitated by the divalent metal ions coordinated by the conserved D-D-E residues.
  3. Integration: The DDE domain also catalyzes the strand transfer reaction, in which the ends of the excised transposon are ligated to the target DNA at a new location. This reaction is also facilitated by the divalent metal ions coordinated by the D-D-E residues. The DDE domain is not limited to DNA transposons. It is also found in the integrase enzymes of retroviruses and certain retrotransposons (Class I transposable elements), where it plays a similar role in catalyzing the integration of the reverse-transcribed cDNA into the host genome. The conservation of the DDE domain across various mobile genetic elements highlights the fundamental importance of this catalytic domain in the transposition process and the evolution of mobile genetic elements across different organisms.
• Donor Primed Replicative Transposition (DPRT): Donor primed replicative transposition is a mechanism used by certain transposable elements, particularly bacterial insertion sequences (IS elements), to move within the genome through a copy-and-paste process. In this model, the transposon is duplicated, and a new copy is inserted into a different location, leaving the original copy in its initial position. This process is also known as replicative transposition. Here's a simplified outline of the donor primed replicative transposition process:
  1. Transcription and translation: The transposable element, such as an IS element, is transcribed into RNA, which is then translated into the transposase protein. This enzyme is responsible for the mobility of the transposable element.
  2. Formation of a synaptic complex: The transposase binds to the terminal inverted repeats (TIRs) at the ends of the transposable element and brings the two ends of the element together to form a synaptic complex.
  3. Cleavage and replication: The transposase cleaves one strand of the donor DNA at each end of the transposable element, creating free 3' hydroxyl groups. The 3' hydroxyl groups then serve as primers for DNA replication, which generates a new copy of the transposable element.
  4. Strand transfer: The newly synthesized transposable element is inserted into the target DNA through a process called strand transfer. In this process, the target DNA is cleaved, and the transposable element is ligated into the new location.
  5. Repair and ligation: The gaps in the target DNA and the donor DNA are repaired by the cellular DNA repair machinery, and the transposable element is ligated into the new location. As a result, the original transposable element remains in its initial position, while the newly synthesized copy is inserted into a different location in the genome. This mechanism allows mobile genetic elements, such as IS elements, to proliferate within the genome, contributing to genomic diversity and evolution. However, it can also cause genomic instability, disrupt genes, or promote the transfer of antibiotic resistance genes among bacteria.

G

• Group II introns: Group II introns are a class of self-splicing introns found in the genomes of bacteria, archaea, and eukaryotic organelles, such as mitochondria and chloroplasts. Introns are non-coding sequences within genes that must be removed during the process of RNA splicing to generate mature, functional RNA molecules. Group II introns are distinct from other types of introns, such as group I introns and spliceosomal introns, due to their unique structural and functional characteristics. Group II introns have several key features:
  1. RNA structure: Group II introns fold into a highly conserved secondary and tertiary RNA structure composed of six domains (labeled DI to DVI). These domains are organized around a central catalytic core that mediates the splicing reaction. The conserved structure of group II introns enables them to perform their self-splicing function.
  2. Self-splicing mechanism: Group II introns are capable of self-splicing, meaning that they can catalyze their own removal from precursor RNA molecules without the need for additional protein factors. The splicing reaction occurs through a two-step transesterification mechanism, which results in the excision of the intron and the ligation of the flanking exons.
  3. Mobility: Some group II introns are mobile genetic elements that can move within the genome through a process called retrohoming or retrotransposition. Mobility is facilitated by an intron-encoded protein (IEP) that has reverse transcriptase, RNA splicing, and sometimes endonuclease activities. During retrohoming, the IEP binds to the intron RNA and promotes reverse transcription of the excised intron into cDNA, which is then integrated into a new genomic location, usually at a homologous target site. This process is similar to the mobility of retrotransposons (Class I transposable elements).
  4. Evolutionary significance: Group II introns are thought to have played a role in the evolution of eukaryotic spliceosomal introns, as they share similarities in their splicing mechanisms and the conserved sequences at their 5' and 3' splice sites. It has been proposed that the spliceosome, a large ribonucleoprotein complex responsible for the splicing of eukaryotic nuclear pre-mRNA, may have evolved from group II introns and their associated proteins. Although group II introns are not as prevalent as spliceosomal introns in eukaryotic nuclear genomes, they play important roles in the gene expression and genome evolution of bacteria, archaea, and eukaryotic organelles. Moreover, their unique self-splicing and mobility properties have made them an interesting subject of study for molecular biologists and evolutionary biologists alike (see also).
• Genome decay: Genome decay is a process that occurs when an organism's genome undergoes genetic deterioration over time, usually as a result of mutation accumulation, deletion of functional genes, or a decrease in the efficacy of natural selection. Genome decay can lead to the loss of gene function, reduction in genome size, and, in some cases, the eventual extinction of a species or population. Genome decay is often observed in the genomes of parasites, endosymbionts, and organisms that have recently undergone a major shift in lifestyle or habitat. Several factors can contribute to genome decay:
  1. Genetic drift: In small populations, random fluctuations in the frequency of genetic variants can lead to the fixation of slightly deleterious mutations. As these mutations accumulate over time, the overall fitness of the population may decrease, contributing to genome decay.
  2. Relaxed selection: When an organism experiences a significant change in its environment or lifestyle, such as adopting an obligate parasitic or endosymbiotic lifestyle, some genes may no longer be essential for survival. In such cases, the selective pressure to maintain these genes is reduced, leading to the accumulation of deleterious mutations and eventual gene loss.
  3. Muller's ratchet: This phenomenon occurs in asexual populations or populations with low rates of recombination. In these cases, deleterious mutations can accumulate in the genome due to a lack of genetic recombination, which would otherwise allow for the removal of harmful mutations through recombination with other individuals.
  4. Repetitive elements and transposons: The presence of repetitive elements and transposable elements in the genome can contribute to genome decay through the promotion of chromosomal rearrangements, such as deletions, duplications, and inversions. These rearrangements can lead to the disruption of functional genes or regulatory regions, resulting in the loss of gene function. Genome decay can have various consequences for an organism:
  5. Loss of gene function: As functional genes accumulate deleterious mutations or are deleted from the genome, the organism may lose the ability to perform certain biological processes, potentially affecting its overall fitness.
  6. Reduced genome size: Genome decay can lead to a reduction in genome size as nonessential genes are lost. This is often observed in the genomes of endosymbionts and parasites, which have smaller genomes compared to their free-living relatives.
  7. Increased dependency: In the case of parasites and endosymbionts, genome decay can lead to an increased dependency on their host for the provision of essential nutrients and metabolites, as the genes required for their synthesis are lost.
  8. Extinction: In extreme cases, the accumulation of deleterious mutations and gene loss due to genome decay can lead to the extinction of a species or population, as its overall fitness decreases to a point where it can no longer survive or reproduce. Understanding genome decay is essential for studying the evolution and adaptation of organisms, particularly in the context of host-parasite and host-endosymbiont interactions. Additionally, knowledge of genome decay can inform the development of strategies for preserving genetic diversity and preventing species extinction.
• Genome Rearrangements: Genome rearrangements are structural changes in the DNA sequence of an organism's genome that involve the reorganization of large DNA segments. These rearrangements can result from various processes, such as DNA breakage and repair, replication errors, or the activity of mobile genetic elements like transposons. Genome rearrangements can have significant consequences for an organism, as they can alter gene structure, regulation, and function, leading to phenotypic changes, adaptation, or, in some cases, disease. There are several types of genome rearrangements:
  1. Deletions: Deletions occur when a segment of DNA is removed from the genome. This can lead to the loss of one or more genes or regulatory elements, potentially resulting in a loss of gene function or altered gene expression.
  2. Duplications: Duplications involve the generation of an extra copy of a DNA segment. Gene duplications can give rise to new gene functions or lead to an increase in gene dosage, which may have adaptive benefits or cause genetic imbalances.
  3. Inversions: An inversion rearranges a DNA segment by flipping it in the reverse orientation relative to the surrounding sequence. Inversions can disrupt genes or alter their regulatory context, potentially affecting gene function or expression.
  4. Translocations: Translocations involve the exchange of DNA segments between non-homologous chromosomes. These rearrangements can disrupt genes, create chimeric genes, or alter gene regulation, and have been implicated in various genetic diseases and cancers.
  5. Insertions: Insertions occur when a DNA segment is added to the genome. This can result from the integration of mobile genetic elements, such as transposons, or the insertion of exogenous DNA, such as viral DNA. Insertions can disrupt genes, alter regulatory elements, or cause genomic instability. Genome rearrangements can have various consequences for an organism:
  6. Evolution and adaptation: Genome rearrangements can generate genetic diversity, providing raw material for natural selection to act upon. In some cases, rearrangements may confer adaptive benefits, such as the acquisition of new gene functions or resistance to environmental stressors.
  7. Disease: Some genome rearrangements can lead to genetic diseases or predispose individuals to certain conditions. For example, translocations are frequently associated with various types of cancer, while large-scale deletions or duplications can cause developmental disorders or intellectual disabilities.
  8. Speciation: Genome rearrangements can contribute to reproductive isolation between populations by creating genetic incompatibilities or chromosomal barriers to gene flow, potentially leading to the formation of new species. Studying genome rearrangements is important for understanding the mechanisms of genome evolution, adaptation, and disease. Advances in DNA sequencing technologies and computational methods have facilitated the detection and characterization of genome rearrangements, providing valuable insights into their roles in biology and medicine.

H

• Horizontal gene transfer (or Lateral gene transfer): Horizontal gene transfer (HGT), also known as lateral gene transfer (LGT), is a process by which genetic material is exchanged between organisms, rather than being directly inherited from a parent organism through reproduction. This transfer of genetic material can occur across different species or even across different domains of life, such as between bacteria and archaea. HGT plays a significant role in the evolution of microorganisms, particularly in the spread of antibiotic resistance genes among bacteria. It can also facilitate the acquisition of new metabolic capabilities or other adaptive traits, allowing organisms to rapidly adapt to new environments. There are three main mechanisms of horizontal gene transfer:
  1. Transformation: In this process, an organism takes up free DNA molecules from the environment, which may integrate into its own genome. This can occur naturally, or it can be artificially induced in a laboratory setting, such as with bacterial transformation for cloning purposes.
  2. Conjugation: This process involves direct cell-to-cell contact between two organisms, typically bacteria. One bacterium transfers a copy of a plasmid (a small, circular DNA molecule) to another bacterium through a tube-like structure called a pilus. The recipient bacterium can then incorporate the plasmid into its own genome, potentially gaining new genes.
  3. Transduction: This process involves the transfer of genetic material between organisms via viruses, specifically bacteriophages (viruses that infect bacteria). A bacteriophage infects a bacterium and accidentally packages bacterial DNA into its viral particles during the viral replication process. When the bacteriophage infects a new host, it can transfer the captured bacterial DNA to the new host, potentially integrating it into the recipient's genome. Horizontal gene transfer has significantly impacted our understanding of microbial evolution, as it enables rapid adaptation and diversification within populations.
• Homologous recombination: Homologous recombination is a fundamental DNA repair and recombination process that occurs in all living organisms, including bacteria, archaea, and eukaryotes. It plays a crucial role in maintaining genomic integrity and stability by repairing DNA double-strand breaks and ensuring the proper segregation of chromosomes during meiosis. Homologous recombination also contributes to genetic diversity by promoting the exchange of genetic material between homologous chromosomes. The homologous recombination process involves the following steps:
  1. DNA double-strand break (DSB) recognition and processing: When a DSB occurs in the DNA, it is recognized by various repair proteins. The broken DNA ends are then processed by nucleases, which remove a stretch of the 5' strand at each break, leaving 3' single-stranded DNA (ssDNA) tails.
  2. Strand invasion and pairing: The exposed ssDNA tails are coated with a recombinase protein, such as RecA in bacteria or Rad51 in eukaryotes, which facilitates the search for a homologous DNA sequence (usually found on a sister chromatid or homologous chromosome) to serve as a repair template. Once a homologous sequence is found, the recombinase-promoted strand invasion occurs, forming a structure called a displacement loop (D-loop).
  3. DNA synthesis and branch migration: DNA polymerases use the invaded strand as a template to synthesize new DNA, extending the 3' end of the invading strand. The D-loop may continue to expand through a process called branch migration, which involves the continuous exchange of DNA strands between the two homologous molecules.
  4. Resolution: The recombination intermediates can be resolved in two different ways, generating either crossover or non-crossover products. Crossover resolution results in the reciprocal exchange of genetic material between the two homologous DNA molecules, while non-crossover resolution restores the original DNA molecules without any exchange. The resolution step is carried out by specific enzymes called resolvases or structure-specific nucleases. Homologous recombination is essential for maintaining genomic stability, repairing DNA damage, and generating genetic diversity during sexual reproduction. Defects in homologous recombination can lead to genomic instability, an increased risk of cancer, and impaired fertility. Understanding the mechanisms of homologous recombination has important implications for our understanding of DNA repair, genome evolution, and the development of targeted therapies for diseases caused by defects in DNA repair pathways.

I

• Inverted Repeats (IR): Inverted repeats are sequences of nucleotides in DNA that are present in two copies, with one being the reverse complement of the other. These sequences are often found at the boundaries of mobile genetic elements such as transposons and insertion sequences, which can move within a genome or between genomes.
• Integron: Integrons are genetic elements found in bacterial genomes that can capture, incorporate, and express genes called gene cassettes. They play a crucial role in the horizontal transfer of genes, particularly antibiotic resistance genes, among bacteria. Integrons are considered a major contributing factor to the rapid spread of antibiotic resistance in bacterial populations. An integron typically consists of the following components:
  1. Integrase gene (intI): This gene encodes an enzyme called integrase, which is responsible for the site-specific recombination of gene cassettes into the integron. Integrase facilitates the insertion and excision of gene cassettes, allowing the bacteria to acquire new genes and potentially new functions.
  2. Primary recombination site (attI): This site is recognized by the integrase enzyme, where the gene cassettes are inserted. Gene cassettes have their own recombination site (attC), and the integrase catalyzes the recombination between the attI and attC sites, leading to the incorporation of the gene cassette into the integron.
  3. Promoter (Pc): A promoter region upstream of the integrase gene is responsible for the transcription of the captured gene cassettes, allowing the expression of the genes within the cassettes. Gene cassettes are small, mobile DNA elements that typically contain a single gene and an attC site. The genes within these cassettes often provide a selective advantage to the bacterial host, such as antibiotic resistance or the ability to metabolize specific compounds. When gene cassettes are integrated into an integron, they are organized in an array, and the expression of the genes is typically driven by a promoter within the integron. Integrons are often associated with plasmids, transposons, and other mobile genetic elements, which can facilitate their transfer between different bacterial species. This, in turn, can contribute to the rapid dissemination of antibiotic resistance and other adaptive traits in bacterial populations. (see also)

M

• Mobilome: The mobilome refers to the entire collection of mobile genetic elements within a genome, an organism, or an ecological community. Mobile genetic elements are DNA sequences that can move within a genome or between genomes, playing a significant role in shaping the structure, function, and evolution of genomes. They contribute to genetic diversity and the adaptation of organisms to new environments.
• Methylase (Methylation): A methylase, also known as a DNA methyltransferase, is an enzyme that adds a methyl group (CH3) to a specific target molecule, such as DNA or RNA. Methylation is the process by which a methyl group is added to a molecule, usually as a means of regulation or modification. In the context of DNA methylation, methylases specifically target certain nucleotides, typically cytosine or adenine bases, and add a methyl group to the carbon or nitrogen atoms of these bases. DNA methylation is an important epigenetic modification that can have various effects on gene expression and cellular function. DNA methylation can either activate or repress gene expression, depending on the specific context and genomic location of the methylation. In bacteria, DNA methylation also plays a crucial role in the restriction-modification (R-M) system, which serves as a defense mechanism against foreign DNA, such as that introduced by bacteriophages. In this system, methylases recognize specific sequences in the host's genomic DNA and methylate them to protect the DNA from cleavage by restriction enzymes. Meanwhile, the restriction enzymes recognize and cleave the same specific sequences in the foreign DNA, which lacks the protective methylation. In summary, a methylase is an enzyme that catalyzes the methylation of DNA or RNA by adding a methyl group to specific target molecules, playing a significant role in gene regulation, cellular function, and bacterial defense mechanisms.

P

• Plasmidome: The plasmidome refers to the entire collection of plasmids present within a single organism or an ecological community, such as a microbial community in a specific environment.
• plasmid F: Plasmid F, also known as the F (fertility) plasmid or F factor, is a circular, double-stranded DNA molecule found in certain strains of Escherichia coli and other enterobacteria. F plasmids are part of the larger family of conjugative plasmids, which are autonomously replicating genetic elements that can transfer between bacterial cells through a process called bacterial conjugation. The F plasmid carries genes that confer several important functions:
  1. Conjugation: The F plasmid contains a set of genes called the tra (transfer) operon, which encodes the proteins required for conjugation. During conjugation, a donor bacterium containing the F plasmid (F+) forms a direct connection with a recipient bacterium without the F plasmid (F-) through a specialized structure called a conjugative or sex pilus. This connection allows for the transfer of a single-stranded copy of the F plasmid from the donor to the recipient cell, converting the recipient into an F+ cell.
  2. Replication: The F plasmid carries genes necessary for its autonomous replication within the host bacterium, ensuring that it is stably maintained and passed on to daughter cells during cell division.
  3. Control of plasmid copy number: The F plasmid also contains genes that regulate its copy number within the host cell, preventing over-replication and ensuring that an optimal number of plasmid copies are maintained. The presence of an F plasmid can have various consequences for the host bacterium:
  4. Fertility: F+ bacteria can serve as donors in conjugation, allowing them to transfer genetic material, such as plasmids or chromosomal DNA, to other bacterial cells. This can promote the spread of genes that confer beneficial traits, such as antibiotic resistance or the ability to utilize novel nutrient sources.
  5. Recombination: Conjugation can facilitate the exchange of genetic material between bacterial cells, promoting recombination and the generation of genetic diversity.
  6. Cost of plasmid maintenance: The presence of an F plasmid imposes a metabolic cost on the host bacterium, as resources must be allocated to plasmid replication and maintenance. However, the benefits of conjugation and the potential for acquiring advantageous genes can outweigh the costs of plasmid maintenance in certain environments. The F plasmid has been extensively studied as a model system for understanding bacterial conjugation, gene transfer, and plasmid replication. It has also been used as a tool in genetic engineering and molecular biology, as it can facilitate the transfer of engineered DNA sequences or other genetic elements between bacterial cells.
• Pseudogenisation: Pseudogenisation refers to the process by which a functional gene accumulates mutations and loses its ability to produce a functional protein product, ultimately becoming a non-functional or non-expressed genetic element known as a pseudogene. Pseudogenes resemble functional genes in sequence but are typically non-functional due to disruptive mutations such as premature stop codons, frameshifts, or deletions. Pseudogenes can be considered "genomic fossils" as they provide evidence of past gene duplications or other evolutionary events. There are several mechanisms that can lead to the formation of pseudogenes:
  1. Gene duplication: During evolution, genes can be duplicated through processes like unequal crossing-over, retrotransposition, or whole-genome duplication. After duplication, one of the gene copies may become non-functional due to the accumulation of mutations, while the other copy retains its function. This non-functional copy is referred to as a duplicated or unprocessed pseudogene.
  2. Retrotransposition: In this process, a gene transcript (mRNA) is reverse transcribed into cDNA and inserted back into the genome, creating a processed pseudogene. Processed pseudogenes typically lack introns, promoter regions, and other regulatory elements necessary for proper gene expression. They also often acquire disruptive mutations over time, which render them non-functional.
  3. Pseudogenisation by deletion or mutation: Functional genes can accumulate mutations or deletions through various mechanisms, such as replication errors, DNA damage, or the activity of mobile genetic elements. When these alterations result in the loss of gene function, the affected gene becomes a pseudogene. Pseudogenes can have various consequences for an organism:
  4. Loss of gene function: As pseudogenes are non-functional, they do not contribute to the production of functional proteins, potentially affecting an organism's fitness or phenotype.
  5. Evolutionary insights: Pseudogenes can provide valuable information about an organism's evolutionary history, as they represent remnants of once-functional genes that have been rendered non-functional over time.
  6. Regulatory roles: Some pseudogenes have been found to play regulatory roles in gene expression, such as competing for microRNA binding or acting as long non-coding RNAs (lncRNAs) that modulate gene expression.
  7. Disease: In some cases, pseudogenes can contribute to disease. For example, pseudogenes that share high sequence similarity with functional genes can interfere with the proper function or regulation of their functional counterparts, leading to genetic disorders or an increased susceptibility to certain conditions. Studying pseudogenes is essential for understanding the evolution and function of genomes, as well as the potential implications of pseudogenisation for an organism's fitness, adaptation, and disease susceptibility. Advances in genome sequencing and comparative genomics have facilitated the identification and characterization of pseudogenes in various organisms, providing insights into their roles in biology and evolution.
• Peel-and-paste (Single-strand) transposition model: The peel-and-paste transposition model, also known as the single-strand transposition model, describes a specific mechanism of transposition employed by certain mobile genetic elements, particularly the bacterial insertion sequences (IS) of the IS200/IS605 family. In contrast to the more common "cut-and-paste" or "copy-and-paste" transposition models, the peel-and-paste model involves the movement of a single DNA strand, rather than a double-stranded DNA segment. The peel-and-paste transposition process can be divided into several steps:
  1. Recognition and cleavage: The transposase enzyme, which is typically encoded by the insertion sequence, recognizes and binds to specific sequences at the ends of the mobile element. Once bound, the transposase cleaves one strand of the DNA, usually the bottom strand, at the terminal inverted repeat (TIR) of the IS element.
  2. Peeling: After the initial cleavage, the transposase peels the single-stranded DNA (ssDNA) segment from the donor molecule. This ssDNA corresponds to the full length of the mobile element.
  3. Target recognition and strand transfer: The transposase-ssDNA complex then recognizes and binds to a target site in the host genome. The transposase promotes the integration of the single-stranded DNA into the target site by catalyzing a strand transfer reaction, which involves the formation of a covalent bond between the 3' end of the peeled ssDNA and the target DNA.
  4. Repair and synthesis: The host DNA repair machinery fills in the gaps created by the integration of the single-stranded mobile element by synthesizing the complementary DNA strand. This process results in the formation of a double-stranded copy of the insertion sequence at the new genomic location.
  5. Restoration of the donor site: The original donor site is also repaired by the host DNA repair machinery, which fills in the gap left by the peeled ssDNA and restores the double-stranded DNA structure. The peel-and-paste transposition model is less common than the cut-and-paste or copy-and-paste models but represents an interesting variation in the mechanisms employed by mobile genetic elements to move within the genome. The peel-and-paste model has been mainly observed in the IS200/IS605 family of bacterial insertion sequences, and the molecular details of this process are still being elucidated.
• Phage tyrosine integrase: Phage tyrosine integrase is a family of site-specific recombinase enzymes that are encoded by bacteriophages (viruses that infect bacteria). These enzymes play a crucial role in the integration of the bacteriophage genome into the host bacterial chromosome during the lysogenic cycle of temperate phages. The phage tyrosine integrase family is named after the conserved tyrosine residue in their active site, which is essential for their catalytic activity. The integration process mediated by phage tyrosine integrase involves the recognition of specific attachment sites on both the bacteriophage (attP) and the bacterial (attB) genomes. The integrase catalyzes a recombination event between these sites, leading to the insertion of the phage genome into the host chromosome, forming a prophage. This allows the phage genome to be replicated and transmitted along with the host chromosome during cell division. The phage tyrosine integrase can also catalyze the excision of the prophage from the host chromosome, allowing the phage to enter the lytic cycle, where it produces new virions and ultimately lyses the host cell. Phage tyrosine integrases are related to other families of site-specific recombinases, such as serine integrases and the lambda integrase family. They are characterized by their distinct catalytic mechanism, which involves a series of DNA cleavage and strand exchange reactions mediated by the conserved tyrosine residue in their active site.
• Phage serine integrase: Phage serine integrase is a family of site-specific recombinase enzymes that are encoded by bacteriophages (viruses that infect bacteria). These enzymes play a crucial role in the integration of the bacteriophage genome into the host bacterial chromosome during the lysogenic cycle of temperate phages. The phage serine integrase family is named after the conserved serine residue in their active site, which is essential for their catalytic activity. Phage serine integrases are related to other families of site-specific recombinases, such as tyrosine integrases and the lambda integrase family. They are characterized by their distinct catalytic mechanism, which involves a series of DNA cleavage and strand exchange reactions mediated by the conserved serine residue in their active site. This mechanism is different from that of tyrosine integrases, which use a conserved tyrosine residue for catalysis.

R

• Resolution site: Resolution site is a specific DNA sequence recognized by a site-specific recombinase or resolvase enzyme. This site is involved in the resolution of cointegrate structures that form during certain types of transposition events, particularly those that occur through replicative transposition mechanisms. Replicative transposition, as seen in some bacterial transposons and insertion sequences, results in the formation of a cointegrate structure. A cointegrate is an intermediate in which the donor and target replicons (e.g., plasmids or chromosomes) are joined together, with the transposable element present in both replicons. To separate the donor and target replicons and complete the transposition process, the cointegrate structure must be resolved. Resolution is mediated by a site-specific recombinase or resolvase enzyme, which is typically encoded by the transposable element itself. The resolvase recognizes and binds to resolution sites within the transposable element, catalyzing a recombination event that leads to the separation of the donor and target replicons. Resolution sites are crucial for the efficient completion of replicative transposition events, as they enable the resolution of cointegrate structures and the proper segregation of the donor and target replicons. In the absence of functional resolution sites or resolvase activity, cointegrates may persist, potentially leading to genomic instability or other deleterious effects on the host organism. Understanding the role of resolution sites and resolvase enzymes in the context of transposable elements provides insights into the mechanisms underlying replicative transposition and the regulation of mobile genetic elements in bacterial and other genomes.
• Resolvase: Resolvase is a type of site-specific recombinase enzyme involved in the resolution of cointegrate structures formed during certain types of transposition events, particularly those that occur through replicative transposition mechanisms. Resolvases are often encoded by the transposable elements themselves, such as bacterial transposons and insertion sequences. Cointegrates are intermediate structures in which the donor and target replicons (e.g., plasmids or chromosomes) are joined together, with the transposable element present in both replicons. To complete the transposition process, the cointegrate structure must be resolved, separating the donor and target replicons. Resolvase enzymes mediate this resolution process by recognizing and binding to specific DNA sequences called resolution sites within the transposable element. They catalyze a recombination event between these resolution sites, which leads to the separation of the donor and target replicons and the formation of two separate replicons, each containing a copy of the transposable element. Resolvases belong to a larger family of site-specific recombinase enzymes, which are involved in various DNA rearrangement processes, such as phage integration and excision, bacterial conjugation, and the regulation of gene expression in response to environmental signals. These enzymes share a common mechanism of action, in which they promote the exchange of DNA strands between specific DNA sequences to mediate recombination events. Studying resolvase enzymes and their role in the resolution of cointegrate structures is crucial for understanding the mechanisms underlying replicative transposition and the regulation of mobile genetic elements in bacterial and other genomes. Resolvases and other site-specific recombinases have also been used as tools in genetic engineering and synthetic biology, as they can facilitate the precise manipulation of DNA sequences within genomes.
• Rolling-circle transposition model: The rolling-circle transposition model is a mechanism used by some transposable elements, particularly those found in bacteria (IS91 family) and eukaryotes (Helitrons), to move from one location to another within a genome. The name "rolling-circle" is derived from the circular nature of the single-stranded DNA intermediate that forms during this process. Here's an overview of the rolling-circle transposition process:
  1. Recognition and cleavage: The transposase enzyme, which is encoded by the transposable element, recognizes and binds to specific sequences at the ends of the mobile element. Once bound, the transposase cleaves one strand of the DNA (usually the bottom strand) at the terminal inverted repeat (TIR) of the transposable element.
  2. Rolling-circle replication: After the initial cleavage, the 3' end of the cleaved DNA strand is extended by the host replication machinery, which uses the uncleaved strand as a template to synthesize a new complementary strand. As this new strand is synthesized, the original cleaved strand is displaced, forming a circular single-stranded DNA (ssDNA) intermediate containing the full length of the mobile element.
  3. Target recognition and integration: The circular ssDNA intermediate is recognized by the transposase, which then binds to a target site in the host genome. The transposase promotes the integration of the circular ssDNA into the target site through a process called strand transfer, which involves the formation of a covalent bond between the 3' end of the ssDNA and the target DNA. The host DNA repair machinery then fills in the gaps created by the integration of the ssDNA, synthesizing the complementary DNA strand and forming a double-stranded copy of the transposable element at the new genomic location.
  4. Restoration of the donor site: The original donor site is repaired by the host DNA repair machinery, which fills in the gap left by the displaced ssDNA and restores the double-stranded DNA structure.

S

• Synaptic complex: Synaptic complex is a nucleoprotein structure formed during the process of transposition, when a transposase enzyme brings together the ends of the transposable element and the target DNA. The synaptic complex is crucial for the accurate movement of transposable elements within a genome. The synaptic complex ensures that the transposable element is accurately excised from its original location and inserted into a new target site in the genome, playing a critical role in the mobility of transposable elements and their impact on genome evolution and diversity.
• Serine recombinase: The serine recombinases are a family of DNA breaking and rejoining enzymes. Unlike homologous recombination, the serine recombinases promote rearrangements of DNA by breaking and rejoining strands at precisely defined sequence positions (see also).
• Serine Resolvases: The serine resolvases and the closely related invertases, are a group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones
• Single-strand transposition:
• Site-specific recombination:

T

• Target specificity:
• Transposase:
• Transposome: A transposome is a nucleoprotein complex formed during the transposition process, which involves the movement of a transposable element (TE) within a genome. The transposome is composed of the transposase enzyme and the transposable element, typically a DNA transposon. The formation of the transposome is a critical step in the transposition process, as it ensures the accurate excision and integration of the transposable element into a new genomic location. In the transposome, the transposase enzyme specifically binds to the ends of the transposable element, usually at terminal inverted repeats (TIRs) or other specific sequences. The transposase then mediates the formation of a synaptic complex by bringing the ends of the transposable element together with the target DNA, creating a loop-like structure. The transposase cleaves the transposable element from its original location and catalyzes the integration of the element into a new target site in the genome. The transposome ensures that the transposable element is accurately excised from its original location and inserted into a new target site in the genome, playing a critical role in the mobility of transposable elements and their impact on genome evolution and diversity.
• Target Primed Replicative Transposition (TPRT): Target Primed Replicative Transposition (TPRT) is a mechanism of transposition used by some mobile genetic elements, particularly non-long terminal repeat (non-LTR) retrotransposons, such as LINEs (Long Interspersed Nuclear Elements). TPRT is a "copy-and-paste" mechanism that involves the reverse transcription of an RNA intermediate and the integration of the resulting DNA copy into a new genomic location. Here is a brief overview of the TPRT process:
  1. Transcription: The non-LTR retrotransposon is transcribed into RNA by the host cell's transcription machinery.
  2. Binding: The RNA molecule binds to an endonuclease and reverse transcriptase encoded by the retrotransposon. This forms a ribonucleoprotein (RNP) complex.
  3. Target site recognition: The RNP complex recognizes and binds to a specific target DNA sequence in the host genome. The endonuclease in the complex nicks one strand of the target DNA, creating a free 3' hydroxyl group.
  4. Reverse transcription: The 3' hydroxyl group of the nicked DNA strand serves as a primer for reverse transcription, which is catalyzed by the reverse transcriptase in the RNP complex. This results in the synthesis of a DNA copy of the retrotransposon RNA, using the RNA molecule as a template.
  5. Second-strand cleavage: The endonuclease in the RNP complex cleaves the second strand of the target DNA, creating a staggered cut. This exposes a new 3' hydroxyl group that serves as a primer for the synthesis of the second DNA strand, complementary to the first DNA copy of the retrotransposon.
  6. Second-strand synthesis: The host DNA repair machinery fills in the gaps created by the staggered cleavage, generating the second DNA strand and completing the insertion of the retrotransposon.
  7. Repair and ligation: The host cell's DNA repair machinery seals any remaining nicks and ligates the newly inserted retrotransposon into the target site. The TPRT mechanism results in the duplication of the mobile genetic element and its insertion into a new genomic location, contributing to genome evolution, diversity, and the expansion of non-LTR retrotransposon families.
• Tyrosine recombinase: Tyrosine site-specific recombinases (YRs) are a family of DNA breaking and rejoining enzymes which use the active site tyrosine nucleophile for DNA strand breakage (see also).

V

• V(D)J Recombination: V(D)J recombination is a process that occurs in the immune system of vertebrates, leading to the generation of diverse antigen receptor repertoires in B and T lymphocytes. While V(D)J recombination is not directly associated with transposable elements, it shares similarities with the mechanisms employed by some transposable elements, particularly in terms of the enzymes involved and the DNA cleavage and rejoining steps. V(D)J recombination involves the rearrangement of variable (V), diversity (D), and joining (J) gene segments to generate diverse immunoglobulin (Ig) genes in B cells and T cell receptor (TCR) genes in T cells. This process is mediated by the recombination-activating genes 1 and 2 (RAG1 and RAG2) that form a complex, known as the RAG recombinase, which recognizes specific recombination signal sequences (RSSs) flanking the V, D, and J gene segments. The similarities between V(D)J recombination and the mechanisms used by some transposable elements are as follows:
  1. Enzymatic machinery: RAG1, the catalytic subunit of the RAG recombinase, has structural and functional similarities with the DDE domain-containing transposases of certain DNA transposons. Both enzyme families use a DDE-like catalytic mechanism to mediate DNA cleavage and rejoining reactions.
  2. DNA cleavage: During V(D)J recombination, the RAG complex introduces a double-strand break (DSB) at the RSSs flanking the V, D, and J gene segments, much like the DSBs introduced by transposases at the ends of DNA transposons.
  3. DNA rejoining: After the DNA cleavage step, the broken DNA ends are rejoined by the non-homologous end-joining (NHEJ) pathway, a cellular DNA repair mechanism. Similarly, DNA transposons are often integrated into new genomic locations through the repair of DSBs by the NHEJ pathway. It is important to note that, despite these similarities, V(D)J recombination and transposable element activity are distinct processes with different biological functions. V(D)J recombination is a tightly regulated process essential for generating immune receptor diversity, whereas transposable elements are mobile genetic elements that can move within the genome and contribute to genomic diversity, evolution, and, in some cases, cause genomic instability. There is evidence suggesting that the RAG1 and RAG2 genes may have evolved from an ancient transposon or transposase gene, supporting the idea that the V(D)J recombination machinery has co-opted a mechanism originally used by mobile genetic elements for a different, essential function in the adaptive immune system.

X

• Xer Site-Specific Recombination: Xer site-specific recombination is a process that occurs in bacteria and involves the resolution of chromosome dimers, which can arise during DNA replication. This recombination mechanism is essential for maintaining the proper segregation of chromosomes during cell division. The Xer recombination system consists of two site-specific recombinases, XerC and XerD, which act on specific DNA sequences called dif sites. Chromosome dimers can form when homologous recombination occurs between two circular sister chromosomes, resulting in the formation of a single circular DNA molecule with two copies of the bacterial chromosome. This can pose a problem during cell division, as the dimeric chromosome cannot be properly segregated between the daughter cells. The Xer site-specific recombination system resolves this issue through the following steps:
  1. Recognition: The XerC and XerD recombinases recognize the dif site, a short DNA sequence that is typically located near the replication terminus of the bacterial chromosome.
  2. Synapsis: XerC and XerD bind to their respective binding sites within the dif site and bring the two dif sites together, forming a synaptic complex.
  3. Strand exchange: The recombinases catalyze a series of strand exchange reactions, in which XerC cleaves one strand of each dif site and exchanges the DNA strands between the two dif sites, followed by XerD-mediated cleavage and strand exchange of the complementary strands.
  4. Resolution: The strand exchange reactions result in the separation of the dimeric chromosome into two monomeric chromosomes, each containing a single copy of the bacterial genome. Xer site-specific recombination is essential for proper chromosome segregation and cell division in bacteria, ensuring the maintenance of genome stability. The Xer recombination system is highly conserved among various bacterial species, highlighting its importance in bacterial genome maintenance. In addition to its role in resolving chromosome dimers, the Xer recombination system has also been implicated in other processes, such as plasmid dimer resolution, integration and excision of mobile genetic elements, and regulation of gene expression.