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Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in bacteria.
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.
Pathogenicity islands (PAIs), as termed in 1990, are a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer. Pathogenicity islands are found in both animal and plant pathogens. Additionally, PAIs are found in both gram-positive and gram-negative bacteria. They are transferred through horizontal gene transfer events such as transfer by a plasmid, phage, or conjugative transposon. Therefore, PAIs contribute to microorganisms' ability to evolve.
A transposase is any of a class of enzymes capable of binding to the end of a transposon and catalysing its movement to another part of a genome, typically by a cut-and-paste mechanism or a replicative mechanism, in a process known as transposition. The word "transposase" was first coined by the individuals who cloned the enzyme required for transposition of the Tn3 transposon. The existence of transposons was postulated in the late 1940s by Barbara McClintock, who was studying the inheritance of maize, but the actual molecular basis for transposition was described by later groups. McClintock discovered that some segments of chromosomes changed their position, jumping between different loci or from one chromosome to another. The repositioning of these transposons allowed other genes for pigment to be expressed. Transposition in maize causes changes in color; however, in other organisms, such as bacteria, it can cause antibiotic resistance. Transposition is also important in creating genetic diversity within species and generating adaptability to changing living conditions.
Lacticaseibacillus caseiis an organism that belongs to the largest genus in the family Lactobacillaceae, a lactic acid bacteria (LAB), that was previously classified as Lactobacillus casei-01. This bacteria has been identified as facultatively anaerobic or microaerophilic, acid-tolerant, non-spore-forming bacteria. The taxonomy of this group has been debated for several years because researchers struggled to differentiate between the strains of L. casei and L. paracasei. It has recently been accepted as a single species with five subspecies: L. casei subsp. rhamnosus, L. casei subsp. alactosus, L. casei subsp. casei, L. casei subsp. tolerans, and L. casei subsp. pseudoplantarum. The taxonomy of this genus was determined according to the phenotypic, physiological, and biochemical similarities.
Site-specific recombinase technologies are genome engineering tools that depend on recombinase enzymes to replace targeted sections of DNA.
In biology, a gene cassette is a type of mobile genetic element that contains a gene and a recombination site. Each cassette usually contains a single gene and tends to be very small; on the order of 500–1000 base pairs. They may exist incorporated into an integron or freely as circular DNA. Gene cassettes can move around within an organism's genome or be transferred to another organism in the environment via horizontal gene transfer. These cassettes often carry antibiotic resistance genes. An example would be the kanMX cassette which confers kanamycin resistance upon bacteria.
Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In humans, approximately 50% of the genome is thought to be MGEs. MGEs play a distinct role in evolution. Gene duplication events can also happen through the mechanism of MGEs. MGEs can also cause mutations in protein coding regions, which alters the protein functions. These mechanisms can also rearrange genes in the host genome generating variation. These mechanism can increase fitness by gaining new or additional functions. An example of MGEs in evolutionary context are that virulence factors and antibiotic resistance genes of MGEs can be transported to share genetic code with neighboring bacteria. However, MGEs can also decrease fitness by introducing disease-causing alleles or mutations. The set of MGEs in an organism is called a mobilome, which is composed of a large number of plasmids, transposons and viruses.
The mobilome is the entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes, prokaryotes, and viruses. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elements in eukaryotes, and plasmids and prophages being the major types in prokaryotes. Virophages contribute to the viral mobilome.
Site-specific recombination, also known as conservative site-specific recombination, is a type of genetic recombination in which DNA strand exchange takes place between segments possessing at least a certain degree of sequence homology. Enzymes known as site-specific recombinases (SSRs) perform rearrangements of DNA segments by recognizing and binding to short, specific DNA sequences (sites), at which they cleave the DNA backbone, exchange the two DNA helices involved, and rejoin the DNA strands. In some cases the presence of a recombinase enzyme and the recombination sites is sufficient for the reaction to proceed; in other systems a number of accessory proteins and/or accessory sites are required. Many different genome modification strategies, among these recombinase-mediated cassette exchange (RMCE), an advanced approach for the targeted introduction of transcription units into predetermined genomic loci, rely on SSRs.
The Tn3 transposon is a 4957 base pair mobile genetic element, found in prokaryotes. It encodes three proteins:
Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.
An origin of transfer (oriT) is a short sequence ranging from 40-500 base pairs in length that is necessary for the transfer of DNA from a gram-negative bacterial donor to recipient during bacterial conjugation. The transfer of DNA is a critical component for antimicrobial resistance within bacterial cells and the oriT structure and mechanism within plasmid DNA is complementary to its function in bacterial conjugation. The first oriT to be identified and cloned was on the RK2 (IncP) conjugative plasmid, which was done by Guiney and Helinski in 1979.
Transposon mutagenesis, or transposition mutagenesis, is a biological process that allows genes to be transferred to a host organism's chromosome, interrupting or modifying the function of an extant gene on the chromosome and causing mutation. Transposon mutagenesis is much more effective than chemical mutagenesis, with a higher mutation frequency and a lower chance of killing the organism. Other advantages include being able to induce single hit mutations, being able to incorporate selectable markers in strain construction, and being able to recover genes after mutagenesis. Disadvantages include the low frequency of transposition in living systems, and the inaccuracy of most transposition systems.
A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Plasmid-mediated resistance is the transfer of antibiotic resistance genes which are carried on plasmids. Plasmids possess mechanisms that ensure their independent replication as well as those that regulate their replication number and guarantee stable inheritance during cell division. By the conjugation process, they can stimulate lateral transfer between bacteria from various genera and kingdoms. Numerous plasmids contain addiction-inducing systems that are typically based on toxin-antitoxin factors and capable of killing daughter cells that don't inherit the plasmid during cell division. Plasmids often carry multiple antibiotic resistance genes, contributing to the spread of multidrug-resistance (MDR). Antibiotic resistance mediated by MDR plasmids severely limits the treatment options for the infections caused by Gram-negative bacteria, especially family Enterobacteriaceae. The global spread of MDR plasmids has been enhanced by selective pressure from antimicrobial medications used in medical facilities and when raising animals for food.
Ruth Milne Hall, OAM, FAA, FAAM is an Australian microbiologist whose research on mobile genetic elements in bacteria has provided deep insight into the transfer and evolution of antibiotic resistance in bacteria.
DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons, that move through an RNA intermediate. DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence. After replicating and propagating in a host, all transposon copies become inactivated and are lost unless the transposon passes to a genome by starting a new life cycle with horizontal transfer. It is important to note that DNA transposons do not randomly insert themselves into the genome, but rather show preference for specific sites.
The AAC/AAD 5' leader is a disputed genetic element that was proposed to be a conserved RNA structure that is found upstream of the bacterial aminoglycosides antibiotic-resistant genes and that functions as an aminoglycoside-specific riboswitch. The putative RNA is upstream of aminoglycoside acetyl transferase (AAC) and aminoglycoside adenyl transferase (AAD) genes.
Integrative and conjugative elements (ICEs) are mobile genetic elements present in both gram-positive and gram-negative bacteria. In a donor cell, ICEs are located primarily on the chromosome, but have the ability to excise themselves from the genome and transfer to recipient cells via bacterial conjugation.
References
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- ↑ Mazel (2006). "Integrons: agents of bacterial evolution". Nature Reviews Microbiology. 4 (8): 608–620. doi:10.1038/nrmicro1462. PMID 16845431. S2CID 4407151.
- 1 2 Hall, Ruth M.; Collis, Christina M. (2006-10-27). "Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination". Molecular Microbiology. 15 (4): 593–600. doi: 10.1111/j.1365-2958.1995.tb02368.x . ISSN 0950-382X. PMID 7783631. S2CID 16476838.
- ↑ MacDonald, Douglas; Demarre, Gaëlle; Bouvier, Marie; Mazel, Didier; Gopaul, Deshmukh N. (2006). "Structural basis for broad DNA-specificity in integron recombination". Nature. 440 (7088): 1157–1162. doi:10.1038/nature04643. ISSN 0028-0836. PMID 16641988. S2CID 4403903.
- ↑ Guerin, Émilie; Cambray, Guillaume; Sanchez-Alberola, Neus; Campoy, Susana; Erill, Ivan; Da Re, Sandra; Gonzalez-Zorn, Bruno; Barbé, Jordi; Ploy, Marie-Cécile; Mazel, Didier (2009-05-22). "The SOS Response Controls Integron Recombination". Science. 324 (5930): 1034. doi:10.1126/science.1172914. ISSN 0036-8075. PMID 19460999. S2CID 42334786.
- ↑ Kovalevskaya, N. P. (2002). "Mobile Gene Cassettes and Integrons". Molecular Biology. 36 (2): 196–201. doi:10.1023/A:1015361704475. S2CID 2078235.
- ↑ Hall R, Collis C, Kim M, Partridge S, Recchia G, Stokes H (1999) Mobile gene cassettes and integrons in evolution.
- ↑ Hall, RM; Collis, CM (1995). "Mobile gene cassettes and integrons: Capture and spread of genes by site-specific recombination". Molecular Microbiology. 15 (4): 593–600. doi: 10.1111/j.1365-2958.1995.tb02368.x . PMID 7783631.
- 1 2 Hall, R. M.; Stokes, HW (2004). "Integrons or super integrons?". Microbiology. 150 (Pt 1): 3–4. doi: 10.1099/mic.0.26854-0 . PMID 14702391.
- ↑ Mazel, D.; Dychinco, B; Webb, VA; Davies, J (1998). "A Distinctive Class of Integron in the Vibrio cholerae Genome". Science. 280 (5363): 605–8. Bibcode:1998Sci...280..605M. doi:10.1126/science.280.5363.605. PMID 9554855.
- ↑ Loot, Céline; Nivina, Aleksandra; Cury, Jean; Escudero, José Antonio; Ducos-Galand, Magaly; Bikard, David; Rocha, Eduardo P. C.; Mazel, Didier (3 May 2017). "Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance". mBio. 8 (2). doi:10.1128/mBio.02296-16. PMC 5371416 . PMID 28351923.
