Transposable elements in E. coli strains.
Mobilomes are all mobile genetic elements (plasmids, transposable elements, insertion sequences, gene cassettes, integrons, genomic islands, and bacteriophages) in a genome. Mobilome is one of the responsible agents for the bacterial evolution, virulence, and increasing antibiotic resistance. The mobile genetic elements in the Escherichia coli genome can carry antibiotic resistance genes and/or virulence genes. The acquisition of new mobile genetic elements can lead to the emergence of new pathotypes. The aim of this chapter is to gather knowledge about mobile genetic elements in E. coli strains. The method in this chapter depends on a literature survey, which scans reviews, research articles, and theses published about transposable elements, plasmids, bacteriophages, and genomic islands in E. coli strains.
- Escherichia coli
- genomic island
1. Introduction to mobilome and mobile genetic elements
Mobilome encompasses all mobile genetic elements (MGEs) in a genome . Mobile genetic elements are moveable DNA segments, transferring among bacterial genomes. MGEs carry the so-called noncore genes and they have an important contribution to the plasticity of bacterial genomes. Plasmids, transposable elements, insertion sequences, gene cassettes, integrons, genomic islands, and bacteriophages are MGEs. Approximately, 2000 genes from 20 sequenced
The presence and/or absence of MGEs within genomic DNA can lead to variance in
The most studied MGEs are transposable elements, plasmids, bacteriophages, and genomic islands in
2. Transposable elements or transposons
Transposable elements (TEs) or transposons have a significant role in the genome evolution and organization . TEs are DNA fragments, which are able to change their position within the genome, in the process called transposition . Bacterial transposable elements or bacterial transposons are divided into three different types: (i) insertion sequence elements, (ii) composite transposons, and (iii) noncomposite transposons. Insertion sequence elements, or in short, insertion sequences (ISs) are the simplest version of the transposable elements. ISs have not genetic information apart from necessary for their mobility. Composite and noncomposite transposons, on the other hand, also they have additional genetic material unrelated with transposition, for example, antibiotic resistance genes . Composite transposons are flanked by the insertion sequences .
Sometimes transposable elements comprise integrons, which are genetic elements that can capture genes including antibiotic resistance from different sources . And integrons can be located on transposons, but also on plasmids, and in the bacterial chromosome . Integrons are genetic elements that include the gene for the enzyme integrase together with gene cassettes encoding antibiotic resistance genes. A study reported a novel integron, In
Plasmids are extrachromosomal DNA elements, which are self-replicating. Apart from the genetic information needed for the autonomous replication, they can also carry additional genetic information like antibiotic resistance genes and the genes encoding resistance to heavy metals, virulence, and other metabolic functions [22, 29]. Thanks to their specific functions, certain plasmids are used as cloning vectors in the recombinant DNA technology . Plasmids are grouped into different Inc families/groups. Inc groups are based on the inability of two plasmids to co-exist together in a bacterial cell . Inc plasmids of the same Inc group have same type of replication region and thus have incompatible replication and partition mechanisms and hence cannot co-exist in a bacterial cell . Plasmids belonging to the IncX family encode various resistance genes, mainly distributed among members of
The paradigm F plasmid, found among members of
Sometimes, plasmids are transferred among bacteria with conjugation, a genetic transfer that occurs between donor and recipient cell that is in a direct cell-to-cell contact . Conjugative plasmids can carry integrons and/or transposons, and such genetic information can be transferred then horizontally via conjugation . Therefore, the spreading of multiresistant genes is promoted . For example, a conjugative
In addition to carrying antibiotic resistance genes, plasmids have a major role in the transfer of virulence-associated genes. One of the most significant
|Name or class||Description/gene carried||Reference|
|IncA/C plasmids||Multiple antibiotic resistance|||
|IncA/C or IncI1 plasmid|||
|Incl2, IncX4, and IncHI2 plasmid|||
|pCERC3||A colV plasmid carrying Sul3-related integron|||
|pAA||Encoding aggregative adherence fimbriae variant|||
|Support of the translocation of the Stx2a across the epithelial cell|||
|pS88||Encoding virulence genes |||
|pO157||Encoding enterohemolysin, serine protease, type II secretion protein, catalase, peroxidase, toxinB|||
|pED1169||Encoding F4-like fimbriae|||
|pGXEC3||Conjugative plasmid harboring |||
|pE80||Conjugative IncFII plasmid encoding |||
Viruses that are infecting bacteria are called bacteriophages. They have a significant impact on the dissemination of antibiotic resistance and virulence-associated genes among foodborne pathogens, as they can transfer genes among bacteria in the process called phage-mediated transduction. Hence, they not only shape the bacterial evolution, but also cause the emergence of new pathogenic bacteria. On the other hand, in a good sense, phages protect against bacterial colonization of mucosal surfaces . Moreover, viruses can be found everywhere in the world including soils, oceans, sewage, and different microbial communities [57, 58]. Transduction can be mediated via virulent or temperate phages. In the case of virulent phages, essentially any region of the bacterial DNA can be transferred (generalized transduction), while temperate phages can transfer only certain genes that are close to the attachment site of the lysogenic phage in the bacterial chromosome (specialized transduction). Specialized transduction happens when the prophage excision is inaccurate and some bacterial DNA co-excised with the prophage DNA . Transduction is a significant process in terms of transferring antimicrobial resistance genes among bacterial cells . For example, the phage called 933E transferred tetracycline resistance gene from the
Furthermore, phages also have the ability to disseminate virulence factors such as staphylokinase, phospholipase or DNase, and superantigens . Phages, which have been known for several years including bacteriophage 𝛌, have been found to carry not only bacterial adhesion genes but also bacterial survival genes [63, 64]. Additionally,
|P1-like bacteriophage (RCS47)|||
|Phage PP01||Two tail fiber genes- 37 and 38 responsible for host-cell recognition|||
5. Genomic islands
Genomic island (GI) is a large region of genomic DNA, more than 10 kb length, which can be frequently exchanged between bacterial isolates. GIs are encoding proteins for transfer, recombination, and restriction/modification or other proprieties, for example, gene clusters for metabolic adaptation, virulence, and or resistance of bacteria . GIs involving virulence-associated genes are called pathogenicity islands (PAIs) . PAI generally encodes genes related to virulence factors (VFs) including adhesins, toxins, invasins, capsule biosynthesis machinery, iron uptake system, and type III, IV, VI and or VII secretion apparatus . Generally, the size of PAIs more than 10 kb and their GC content differs from the average genome. Their integration site is located in tRNA genes and repeated sequences, which is containing at least one mobile genetic element including remnants of plasmids, insertion sequences (ISs), and integrons, and associated gene cassettes . tRNA-encoding genes are known as the hot spot for the integration of foreign DNA . Several PAIs can be excised from bacterial chromosome by site-specific recombination .
PAIs have been reported firstly in the genome of uropathogenic
Enterocyte effacement locus (LEE) is one of the best known PAIs in
|LEE||PAI locus of enterocyte effacement|||
|Yersiniabactin-HPI||Encoding an siderophore iron uptake system|||
|PAI I536 and PAI II536||Hemolysin and P fımbriae|||
|PAI III536 and PAI IV536||S fimbriae and HPI|||
|PAI V536||K15 capsule determinant|||
|Vat-encoding PAI||Adjacent to the 3′ terminus-thrW tRNA gene|||
|EPAI1||RTX family exoprotein|||
|EPAI2||O-antigen polysaccharide (OPS)|||
|AGI-3 PAI||SelC-associated GI involved in carbohydrate uptake and virulence|||
|GI OI-29||Transcriptional activator GmrA|||
It was reported that UPEC strain 536 has at least four PAIs located on the chromosome. The sizes of the first two PAI I536 and PAI II536 are 70 and 120 kb. The significant virulence-associated genes encoded on these PAIs are hemolysin and P fimbriae. PAI III536 and PAI IV536 have S fimbriae and HPI analog gene clusters . It was reported that an ExPEC strain causing neonatal meningitis possessed the HPI, suggesting that HPI was associated with the development of neonatal meningitis . Moreover, capsule synthesis-associated genes can be located on different PAIs in ExPEC . Furthermore, it was shown that HPI in general contributes to ExPEC virulence . Another novel PAI was found in an APEC strain integrated adjacent to the thrW tRNA gene encoding vacuolating autotransporter toxin. This PAI is known as Vat-encoding pathogenicity island and may contribute to APEC pathogenicity . A novel function carried by a GI was reported recently—a GI located in the EHEC chromosome included the transcriptional activator GmrA that controls the motility of EHEC O157:H7 . In addition, GIs have a role not only in virulence but also in the metabolic process of the bacterial cell. The
This study was supported by a fellowship from the Program (TUBITAK-2219-2017-2nd term), and Elif Bozcal was awarded a fellowship by the Scientific and Technological Research Council of Turkey.
Conflict of interest
The author has no conflict of interest.