New genetic material can come into the bacteria either by an internal genetic mutation i.e. de novo or can be acquired from an external source that is through horizontal gene transfer (HGT). This allows the bacteria to rapidly acquire complex new traits and is a key to drive bacterial evolution. Natural transformation, conjugation and transmissible mobile genetic elements such as plasmid, transposons and bacteriophages are the primary mechanisms for exchange of genetic elements. In transformation DNA from one organism is released into the environment. This DNA is taken up by another organism that is capable of recognizing and binding DNA. Conjugation requires actual contact between donor and recipient cells. The donor cell synthesizes a multiprotein apparatus known as mating pair and enables the transfer of DNA. Plasmids are extrachromosomal piece of DNA. They are capable of replicating by themselves. Transposons are highly mobile segments of DNA. They are capable of moving from one part of the DNA to another. Bacteriophage or virus phages can move also move DNA from one organism to another. If recombination occurs, the genes which are coding for the virulence factor may become chromosomal and express themselves. Pathogenicity islands are a large group of genes that are associated with pathogenicity and are located on the bacterial chromosome. Mobile genetic elements have a huge impact on the overall bacterial genome as they change the genome size as well as the pathogenicity. They play a major role even in the bacterial evolution and contribute even to the adaptation to newer environments and the changing ecological niches. The mobile genetic elements even transfer virulence factors as well as antimicrobial resistance genes.
The mobile integrative mobile genetic elements can be grouped into five major classes: insertion sequence-like transposons, integrative-conjugative elements, proviruses, casposons and cryptic integrated elements.
In 1970s, transposons were first discovered in bacteria. The DNA elements or segments that can move that is, transpose from one place in the bacterial DNA to another are called transposons. The smallest which is called insertion sequence (IS) elements. Transposons have a transposase gene, encoding an enzyme that promotes their transposition. They also have an inverted -repeat sequences at their ends. These repeated sequences are used to target IS sites in the DNA of the host. The repeated end sequences can also contain promoters that point outward from the IS element. This drive the expression of adjacent genes on the chromosome. Larger transposons can encode other genes which include selectable markers such as antibiotic resistance genes or virulence factors like biosynthetic genes for polysaccharide capsule or toxin genes. Conjugative transposons, also carry tra genes that can promote transfer of their own DNA along with other small mobilizable DNA elements that are present in the same strain. Conjugative transposons also have genes for proteins that promote integration into or excision from the chromosome. Conjugative transposons and plasmids can transfer systems that enable them to move DNA between unrelated species, as well as between like species.
Integrative and conjugative elements. [ICEs]
Integrative and conjugative elements are mobile genetic elements that are very similar to transposons, bacteriophages and plasmids. They are able to integrate into the bacterial chromosomes. Under certain conditions, they can even excise from the chromosome and be transferred to from one bacterium to another by conjugation but they are not able to replicate by themselves. They integrate these elements into the bacterial chromosome at specific sites and frequently occurs at the 3’ end of the t-RNA gene. Once they integrate, they can replicate as a part of bacterial chromosome. These elements transfer a large amount of genetic material, including virulence encode genes. All the ICEs encode an integrase that are able to integrate into the bacterial host chromosome. Integrase are necessary to mediate integration and are also required for excision. Integrase decides the site where the ICEs can be integrated and even the point of excision. The integrase are members of the tyrosine recombinase family. The best studied recombinase is the lambda phage. The recombinase uses a topoisomerase like mechanism to promote site specific recombination between identical and nearly identical sequences in the host chromosome which is referred to as the attP and the phage chromosome which is referred to as attB site. The kind of integrase can vary among various organisms and can be further subdivided into various subclasses even though they are present in diverse host back grounds. Even after the variation the integrase, they mediate integration at the 3’ ends of the tRNA loci only. For example, Mesorhizobium loti [ICEMlSymR7A], H. influenzae [ ICEHin1056], etc. The integration at the attB site is a preference not an absolute dependence. Sometimes it can integrate at various other sites too.
E. coli has a core of essential genes and an accessory genome that contain the adaptability genes. They are aggregated over time as a result of gain and loss of genes from the environment. The genome of pathogenic E. coli O157:H7 strain encodes over 1600 proteins and 20 tRNAs these genes are not found in non-pathogenic E. coli strain K-12, and most of the O157-specific proteins are encoded by prophages and prophage-like elements. The mobile genetic elements like plasmids, phage, and PAIs transferred to non-pathogenic E. coli have created a range of pathogens that cause a variety of diseases. Enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) are both characterized by their ability to form attaching and effacing lesions in the intestine. EHEC cause bloody diarrhoea and toxemia in human. EHEC Serotype O157:H7 have virulence factors, which evolved from an EPEC by acquisition of a bacteriophage that carries the stx gene. Enteroaggregative O104:H4 E. coli acquires a plasmid with genes for fimbrial adherence and colonization became infected with a phage carrying the stx gene.
Many bacteriophages associated with virulent strains encode powerful extracellular toxins, effector proteins participating in invasion, various enzymes such as superoxide dismutase, staphylokinase, phospholipase, DNase, proteins affecting resistance to serum and altering antigenicity, superantigens, adhesion factors, proteinases, and mitogenic factors.
· Phages encode various bacterial exotoxins.
A large number of bacterial toxins are found in the genomes of phages that incorporate into the bacterial chromosome. The phage mediated genetic exchange is very restricted sometimes.
The tox-positive phage encodes the diphtheria toxin for Corynebacterium diphtheriae. This diphtheria toxin is also produced by strains of C. ulcerans that carry a tox+ phage, which appears to be originated distinct from that of the phage in C. diphtheriae. The phage encoded diphtheriae toxin is also produced by C. pseudotuberculosis. The regulations of the lysogenic phage are also regulated by the presence of iron. The virulence factor increases in the presence of low concentration of iron. In this way, low concentration of iron can increase the pathogenicity of the organism.
The SaPIs are toxin carrying pathogenicity islands of Staphylococcus aureus. The SaPIs encode the toxic shock toxin [TSST-1] and even other superantigens. Under certain conditions this SaPIs DNA can excise and be packed in a temperate phage head. These genes can then be transferred to various S. aureus strains and also to non-aureus strains. This is possible as the gene can integrate at the secondary site which is homologues, in absence of the primary site. Any bacterium that can absorb the SaPIs helper phage is a potential recipient. The toxic gene can be transduced to S. epidermidis, S. xylosus, L. monocytogenes, etc.
· Phages enhance biofilm formation.
P. aeruginosa is well known for its capacity to produce biofilm. They can colonize water lines and various abiotic surfaces as well. Gram-negative pathogen often colonizes the lungs of cystic fibrosis (CF) patients. The most highly activated genes in P. aeruginosa PAO1 biofilms are those within a filamentous prophage, Pf4. These free phages can be isolated from biofilm effluents from strain PAO1 and other clinical isolates. The deletion of the filamentous phage Pf4 from P. aeruginosa PAO1 prevented the typical lysis also death of bacteria at the late stages of biofilm development. If SCVs are present in the late stages of biofilm development generally correlates with the conversion of Pf4 into a superinfective form. There is an important role of filamentous prophages in modulating biofilm dispersal also in the formation of drug-resistant SCVs, and in the virulence of P. aeruginosa.
· Phages influence bacterial adhesion, colonization and invasion.
Phage-mediates adhesion of Streptococcus mitis which causes infective endocarditis. Bacterial invasion of the human tissues involves the activity of various bacterial enzymes. A streptococcal (GAS) hyaluronidase is encoded with the phage particles themselves. This give an additional advantage as the capsule of GAS is composed solely of hyaluronic acid and helps the organisms to penetrate better.
· Phages enhance bacterial resistance to serum and phagocytosis
E. coli, S.dysenteriae, S.enterica have phages that alter the O antigen by using various enzymes. This helps to enhance their virulence.
Cryptic or “defective” prophages are considered harmless as they are quiescent and most of their genes are be repressed. They have lost their capacity to produce the infectious particles, so they not pose any threat to their host. Cryptic prophages help in modulating biofilm formation in E. coli. The E. coli K-12 strain has around 9 cryptic prophages in its chromosome. If all the nine cryptic genes are removed a cured E. coli strain termed Δ9 is obtained. The greatest impact on biofilm formation is seen in phage remnants e14, rac and CP4–44 are important is biofilm formation after curing E. coli K-12 from any of these remnants impaired biofilm production. The presence of defective prophages can contribute significantly to important bacterial phenotypes such as biofilm formation and drug-resistance.
PAIs are a part of active mobile DNA elements such as plasmids, transposons, or phages. PAIs can provide virulence factors. They provide the host with a selective advantage under certain environmental conditions. These genes may provide new types of pili for altered adhesion. As adherence is the primary and important step to cause any disease. They allowing the bacteria to bind to different tissues and enhance colonization. This also gives the organism a means of acquiring iron and other nutrients. By carrying the genes which are novel to the organism increases the survival rate in the host cell. They can carry genes which encode LPS, help to increased serum resistance provide a capsular biosynthesis to prevent phagocytosis, for delivery of proteins that enhance bacterial invasion or modulate intracellular signalling processes, or even dampen immune responses. PAIs also encode genes of bacterial protein toxin. Most bacterial protein toxin are located on PAIs. Phage or lysogenic prophages carrying toxin genes are a natural reservoir for toxin genes. For example, the cholera toxin gene (ctx), which is carried on a prophage in Vibrio cholerae, is closely related to the heat-labile enterotoxin genes (elt and etx) found in different strains of E. coli that cause diarrhoea. These enterotoxin genes can be found either on a plasmid or on the chromosome, depending on the strain of E. coli. Shiga toxin related (stx) genes can be seen in Shigella as well as E. coli strains. Phage containing stx gene from Shigella and E. coli can be transmitted between different bacteria in the intestines of humans and other animals. It can even be transmitted from external aquatic environments, such as sewage or water and soil contaminated with feaces. Botulinum or tetanus neurotoxin (bot or tet) genes found in different strains and species of Clostridium. There are diverse locations where the PAIs carrying Clostridium botulinum and Clostridium tetani neurotoxin genes are carried. These PAIs can be located on plasmids and lysogenic prophages or as gene clusters on the chromosome depending on the species.
Casposons are a new superfamily of mobile genetic elements. They have many features similar to eukaryotic self-synthesizing DNA transposons. They utilize Cas1 endonucleases for integration into the host genome by CRISPR-Cas immunity. They play an important in the origin of adaptive immunity.
As seen above genes can encode for various virulence factors like adherence, colonization production of various toxins, etc. The genes can not only be shared between organisms of the sample species but also across various different species. This helps the organisms to establish themselves in the host and cause the disease or enhance the survival of the organism.