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 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.
The origin of replication is a particular sequence in a genome at which replication is initiated. This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
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.
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.
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.
A relaxase is a single-strand DNA transesterase enzyme produced by some prokaryotes and viruses. Relaxases are responsible for site- and strand-specific nicks in double-stranded DNA. Known relaxases belong to the Rolling Circle Replication (RCR) initiator superfamily of enzymes and fall into two broad classes: replicative (Rep) and mobilization (Mob). The nicks produced by Rep relaxases initiate plasmid or virus RCR. Mob relaxases nick at origin of transfer (oriT) to initiate the process of DNA mobilization and transfer known as bacterial conjugation. Relaxases are so named because the single-stranded DNA nick that they catalyze lead to relaxation of helical tension.
fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.
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;
The nic site or nick region is found within the origin of transfer (oriT) site and is a key in starting bacterial conjugation.[1]
The traA gene codes for relaxase, which is an enzyme that initiates plasmid DNA transfer during bacterial conjugation. Relaxase forms a relaxosome complex with auxiliary proteins to initiate conjugation. Relaxosome binds to the origin of transfer (oriT) sequence and cleaves the DNA strand that will be transferred.
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.
In molecular cloning, a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell, where it can be replicated and/or expressed. A vector containing foreign DNA is termed recombinant DNA. The four major types of vectors are plasmids, viral vectors, cosmids, and artificial chromosomes. Of these, the most commonly used vectors are plasmids. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.
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.
Bacterial genetics is the subfield of genetics devoted to the study of bacteria. Bacterial genetics are subtly different from eukaryotic genetics, however bacteria still serve as a good model for animal genetic studies. One of the major distinctions between bacterial and eukaryotic genetics stems from the bacteria's lack of membrane-bound organelles, necessitating protein synthesis occur in the cytoplasm.
Plasmids must regulate their copy number to ensure that they do not excessively burden the host or become lost during cell division. Plasmids may be either high copy number plasmids or low copy number plasmids; the regulation mechanisms between these two types are often significantly different. Biotechnology applications may involve engineering plasmids to allow a very high copy number. For example, pBR322 is a low copy number plasmid from which several very high copy number cloning vectors have been derived.
In computing, a Digital Object Identifier or DOI is a persistent identifier or handle used to identify objects uniquely, standardized by the International Organization for Standardization (ISO). An implementation of the Handle System, DOIs are in wide use mainly to identify academic, professional, and government information, such as journal articles, research reports and data sets, and official publications though they also have been used to identify other types of information resources, such as commercial videos.
PubMed Central (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature. As one of the major research databases within the suite of resources that have been developed by the National Center for Biotechnology Information (NCBI), PubMed Central is much more than just a document repository. Submissions into PMC undergo an indexing and formatting procedure which results in enhanced metadata, medical ontology, and unique identifiers which all enrich the XML structured data for each article on deposit. Content within PMC can easily be interlinked to many other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to freely discover, read and build upon this portfolio of biomedical knowledge.
