A pilus is a hair-like appendage found on the surface of many bacteria. The terms pilus and fimbria can be used interchangeably, although some researchers reserve the term pilus for the appendage required for bacterial conjugation. All pili in the latter sense are primarily composed of pilin proteins, which are oligomeric.
A plasmid is a small DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism, such as by providing antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation.
A high-frequency recombination cell is a bacterium with a conjugative plasmid integrated into its chromosomal DNA. The integration of the plasmid into the cell's chromosome is through homologous recombination. A conjugative plasmid capable of chromosome integration is also called an episome. When conjugation occurs, Hfr cells are very efficient in delivering chromosomal genes of the cell into recipient F− cells, which lack the episome.
In molecular biology, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacteria must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory.
Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are caused by the insertion of a small segment of DNA, from a plasmid, into the plant cell, which is incorporated at a semi-random location into the plant genome.
Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis. Triparental matings can help overcome some of the barriers to efficient plasmid mobilization. For instance, if the conjugative plasmid and the mobilizable plasmid are members of the same incompatibility group they do not need to stably coexist in the second bacterial strain for the mobilizable plasmid to be transferred.
A Ti or tumour inducing plasmid is a plasmid that often, but not always, is a part of the genetic equipment that Agrobacterium tumefaciens and Agrobacterium rhizogenes use to transduce their genetic material to plants. The Ti plasmid is lost when Agrobacterium is grown above 28 °C. Such cured bacteria do not induce crown galls, i.e. they become avirulent. pTi and pRi share little sequence homology but are functionally rather similar. The Ti plasmids are classified into different types based on the type of opine produced by their genes. The different opines specified by pTi are octopine, nopaline, succinamopine and leucinopine.
RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homologous DNA repair proteins. The homologous protein is called RAD51 in eukaryotes and RadA in archaea.
In molecular biology, subcloning is a technique used to move a particular DNA sequence from a parent vector to a destination vector.
Resistance transfer factor is an old name for a plasmid that codes for antibiotic resistance. R-factor was first demonstrated in Shigella in 1959 by Japanese scientists. Often, R-factors code for more than one antibiotic resistance factor: genes that encode resistance to unrelated antibiotics may be carried on a single R-factor, sometimes up to 8 different resistances. Many R-factors can pass from one bacterium to another through bacterial conjugation and are a common means by which antibiotic resistance spreads between bacterial species, genera and even families. For example, RP1, a plasmid that encodes resistance to ampicillin, tetracycline and kanamycin originated in a species of Pseudomonas, from the family Pseudomonadaceae, but can also be maintained in bacteria belonging to the family Enterobacteriaceae, such as Escherichia coli.
The fertility factor allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation. The F factor is carried on the F episome, the first episome to be discovered. Unlike other plasmids, F factor is constitutive for transfer proteins due to a mutation in the gene finO. The F plasmid belongs to a class of conjugative plasmids that control sexual functions of bacteria with a fertility inhibition (Fin) system.
Fosmids are similar to cosmids but are based on the bacterial F-plasmid. The cloning vector is limited, as a host can only contain one fosmid molecule. Fosmids can hold DNA inserts of up to 40 kb in size; often the source of the insert is random genomic DNA. A fosmid library is prepared by extracting the genomic DNA from the target organism and cloning it into the fosmid vector. The ligation mix is then packaged into phage particles and the DNA is transfected into the bacterial host. Bacterial clones propagate the fosmid library. The low copy number offers higher stability than vectors with relatively higher copy numbers, including cosmids. Fosmids may be useful for constructing stable libraries from complex genomes. Fosmids have high structural stability and have been found to maintain human DNA effectively even after 100 generations of bacterial growth. Fosmid clones were used to help assess the accuracy of the Public Human Genome Sequence.
Plant transformation vectors are plasmids that have been specifically designed to facilitate the generation of transgenic plants. The most commonly used plant transformation vectors are termed binary vectors because of their ability to replicate in both E. coli, a common lab bacterium, and Agrobacterium tumefaciens, a bacterium used to insert the recombinant (customized) DNA into plants. Plant Transformation vectors contain three key elements;
An origin of transfer (oriT) is a short sequence that is necessary for transfer of the DNA that contains it from a bacterial host to recipient during bacterial conjugation. The oriT is cis-acting — it is found on the same DNA that is being transferred, and it is transferred along with the DNA. The origin of transfer consists of three functionally defined domains: a nicking domain, a transfer domain, and a termination domain.
The nic site or nick region is found within the origin of transfer (oriT) site and is a key in starting bacterial conjugation.[1]
Transfer operon, commonly called tra operon, or tra genes, are some genes necessary for non-sexual transfer of genetic material in both gram-positive and gram-negative bacteria. The tra locus includes the pilin gene and regulatory genes, which together form pili on the cell surface, polymeric proteins that can attach themselves to the surface of F-bacteria and initiate the conjugation. The existence of the tra region of a plasmid genome was first discovered in 1979 by David H. Figurski and Donald R. Helinski In the course of their work, Figurski and Helinski also discovered a second key fact about the tra region – that it can act in trans to the mobilization marker which it affects.
The traJ-II RNA motif is a conserved RNA structure discovered in bacteria by using bioinformatics. traJ-II RNAs appear to be in the 5' untranslated regions of protein-coding genes called traJ, which functions in the process of bacterial conjugation. A previously identified motif known as TraJ 5' UTR is also found upstream of traJ genes functions as the target of FinP antisense RNAs, so it is possible that traJ-II RNAs play a similar role as targets of an antisense RNA. However, some sequence features within the traJ-II RNA motif suggest that the biological RNA might be transcribed from the reverse-complement strand. Thus is it unclear whether traJ-II function as cis-regulatory elements. traJ-II RNAs are found in a variety of proteobacteria.
