Mobile genetic elements
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. They can also rearrange genes in the host genome. One of the examples of MGEs in evolutionary context is that virulence factors and antibiotic resistance genes of MGEs can be transported to share them with neighboring bacteria. Newly acquired genes through this mechanism can increase fitness by gaining new or additional functions. On the other hand, 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.
- Plasmids: These are generally circular extrachromosomal DNA molecules that replicate and are transmitted independent of chromosomal DNA. They are present in prokaryotes (bacteria and archaea) and sometimes in eukaryotic organisms such as yeast. Plasmids during their cycle carry genes from one organism to another through a process called conjugation. They also often inject genes that make bacteria resistant to antibiotics.
- Cloning vectors: These are a type of hybrid plasmids with bacteriophages, used to transfer and replicate DNA fragments that are inserted by means of recombinant DNA techniques. To serve as a vector, it must be able to replicate together with the DNA fragment it carries. Examples are cosmids and phagemids.
- Transposons: These are DNA sequences that can move and replicate in different parts of a cell's genome. Also called "jumping genes" they can be transferred horizontally between organisms that live in symbiosis. Transposons are present in all living things and in giant viruses.
- DNA transposons: These are transposons that move directly from one position to another in the genome using a transposase to cut and stick at another locus.
- Retrotransposons: These are transposons that move in the genome, being transcribed into RNA and later into DNA by reverse transcriptase. Retrotransposons are present exclusively in eukaryotes. These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI [P-element induced wimpy testis]-interacting RNAs (piRNAs). piRNA is a recently discovered class of ncRNAs, which are in the length range of ~24-32 nucleotides. Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) because of their origin from the repetitive elements such as transposable sequences of the genome. However, later it was identified that they acted via PIWI-protein. In addition to having a role in the suppression of genomic transposons, various roles of piRNAs have been recently reported like regulation of 3’ UTR of protein-coding genes via RNAi, transgenerational epigenetic inheritance to convey a memory of past transposon activity, and RNA-induced epigenetic silencing.
- Integrons: These are gene cassettes that usually carry antibiotic resistance genes to bacterial plasmids and transposons.
- Introns: Group I and II introns are nucleotide sequences with catalytic activity that are part of host transcripts and act as ribozymes that can invade genes that encode tRNA, rRNA, and proteins. They are present in all cellular organisms and viruses.
- Viral agents: These are mostly infective acellular agents that replicate in cellular hosts. During their infective cycle they can carry genes from one host to another. They can also carry genes from one organism to another in case that viral agent infects more than two different species. Traditionally they are considered separate entities, but the truth is that many researchers who study their characteristics and evolution refer to them as mobile genetic elements. This is based on the fact that viral agents are simple particles or molecules that replicate and are transferred between various hosts like the remaining non-viral mobile genetic elements. According to this point of view, viruses and other viral agents should not be considered living beings and should be better conceived as mobile genetic elements. Viral agents are evolutionarily connected with various mobile genetic elements.
- Viruses: These are viral agents composed of a molecule of genetic material (DNA or RNA) and with the ability to form complex particles called virions to be able to move easily between their hosts. Viruses are present in all living things. Viral particles are manufactured by the host's replicative machinery for horizontal transfer.
- Satellite nucleic acids: These are DNA or RNA molecules, which are encapsidated as a stowaway in the virions of certain helper viruses and which depend on these to be able to replicate. Although they are sometimes considered genetic elements of their helper viruses, they are not always found within their helper viruses.
- Viroids: These are viral agents that consist of circular RNA molecules that infect and replicate in plants.
- Endogenous viral element: These are viral nucleic acids integrated into the genome of a cell. They can move and replicate multiple times in the host cell without causing disease or mutation. They are considered autonomous forms of transposons. Examples are proviruses and endogenous retroviruses.
CRISPR-Cas systems in bacteria and archaea are adaptive immune systems to protect against deadly consequences from MGEs. Using comparative genomic and phylogenetic analysis, researchers found that CRISPR-Cas variants are associated with distinct types of MGEs such as transposable elements. In addition, CRISPR-Cas controls transposable elements for their propagation.
MGEs such as plasmids by a horizontal transmission are generally beneficial to an organism. The ability of transferring plasmids (sharing) is important in an evolutionary perspective. Tazzyman and Bonhoeffer found that fixation (receiving) of the transferred plasmids in a new organism is just as important as the ability to transfer them. Beneficial rare and transferable plasmids have a higher fixation probability, whereas deleterious transferable genetic elements have a lower fixation probability to avoid lethality to the host organisms.
One type of MGEs, namely the Intergrative Conjugative Elements (ICEs) are central to horizontal gene transfer shaping the genomes of prokaryotes enabling rapid acquisition of novel adaptive traits.
As a representative example of ICEs, the ICEBs1 is well-characterized for its role in the global DNA damage SOS response of Bacillus subtilis and also its potential link to the radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores, isolated from spacecraft cleanroom facilities.
Transposition by transposable elements is mutagenic. Thus, organisms have evolved to repress the transposition events, and failure to repress the events causes cancers in somatic cells. Cecco et al. found that during early age transcription of retrotransposable elements are minimal in mice, but in advanced age the transcription level increases. This age-dependent expression level of transposable elements is reduced by calorie restriction diet.
The consequence of mobile genetic elements can alter the transcriptional patterns, which frequently leads to genetic disorders such as immune disorders, breast cancer, multiple sclerosis, and amyotrophic lateral sclerosis. In humans, stress can lead to transactional activation of MGEs such as endogenous retroviruses, and this activation has been linked to neurodegeneration.
The total of all mobile genetic elements in a genome may be referred to as the mobilome.
Mobile genetic elements play a critical role in the spread of virulence factors, such as exotoxins and exoenzymes, among bacteria. Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed.
- ACLAME (The CLAssification of Mobile genetic Elements) database
- De novo gene birth
- Exon shuffling
- Gene fusion
- Gene duplication
- Horizontal gene transfer
- Virulence factors
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