FACTOID # 27: If you're itching to live in a trailer park, hitch up your home and head to South Carolina, where a whopping 18% of residences are mobile homes.
 
 Home   Encyclopedia   Statistics   States A-Z   Flags   Maps   FAQ   About 
   
 
WHAT'S NEW
 

SEARCH ALL

FACTS & STATISTICS    Advanced view

Search encyclopedia, statistics and forums:

 

 

(* = Graphable)

 

 


Encyclopedia > Plasmid
Figure 1: Illustration of a bacterium with plasmids enclosed showing chromosomal DNA and plasmids.
Figure 1: Illustration of a bacterium with plasmids enclosed showing chromosomal DNA and plasmids.

A plasmid is an extrachromosomal DNA molecule separate from the chromosomal DNA and capable of sexual replication. In many cases, it is typically circular and double-stranded. It usually occurs naturally in bacteria, and is sometimes found in eukaryotic organisms (e.g., the 2-micrometre-ring in Saccharomyces cerevisiae). Image File history File links Plasmid_(english). ... Image File history File links Plasmid_(english). ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... A scheme of a condensed (metaphase) chromosome. ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ... Binomial name Meyen ex E.C. Hansen Saccharomyces cerevisiae is a species of budding yeast. ...


Plasmid size varies from 100 to over 400000 kilobase pairs (kbp). The number of identical plasmids within a single cell can be zero, one, or even thousands under some circumstances. Plasmids can be considered to be part of the mobilome, since they are often associated with conjugation, a mechanism of horizontal gene transfer. Base pairs, of a DNA molecule. ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell being used to describe the smallest unit of a living organism Cells in culture, stained for keratin (red) and DNA (green) The cell is the... The mobilome is the total of all mobile genetic elements in a genome. ... Bacterial conjugation is the transfer of genetic material between bacteria through direct cell-to-cell contact. ... Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. ...


The term plasmid was first introduced by the American molecular biologist Joshua Lederberg in 1952.[1] Molecular biology is the study of biology at a molecular level. ... Joshua Lederberg speaking at a conference in 1997 Joshua Lederberg (born May 23, 1925) is an American molecular biologist who is known for his work in genetics, artificial intelligence, and space exploration. ...


Plasmids can be considered to be independent life-forms similar to viruses, since both are capable of autonomous replication in suitable (host) environments. However the plasmid-host relationship tends to be more symbiotic than parasitic (although this can also occur for viruses, for example with Endoviruses), since plasmids can endow their hosts with useful packages of DNA to assist mutual survival in times of severe stress. For example, plasmids can convey antibiotic resistance to host bacteria, who may then survive along with their life-saving guests who are carried along into future host generations.

Contents

Vectors

Further information: Vector (molecular biology)

Plasmids used in genetic engineering are called vectors. Plasmids serve as important tools in genetics and biochemistry labs, where they are commonly used to multiply (make many copies of) or express particular genes.[2] Many plasmids are commercially available for such uses. Kenyans examining insect-resistant transgenic Bt corn. ... Protein expression is a subcomponent of gene expression. ...


The gene to be replicated is inserted into copies of a plasmid containing genes that make cells resistant to particular antibiotics and a multiple cloning site (MCS, or polylinker), which is a short region containing several commonly used restriction sites allowing the easy insertion of DNA fragments at this location. Next, the plasmids are inserted into bacteria by a process called transformation. Then, the bacteria are exposed to the particular antibiotics. Only bacteria which take up copies of the plasmid survive the antibiotic, since the plasmid makes them resistant. In particular, the protecting genes are expressed (used to make a protein) and the expressed protein breaks down the antibiotics. In this way the antibiotics act as a filter to select only the modified bacteria. Now these bacteria can be grown in large amounts, harvested and lysed (often using the alkaline lysis method) to isolate the plasmid of interest. A multiple cloning site (MCS), also called a polylinker, is a short segment of DNA which contains many (usually 20+) restriction sites - a standard feature of engineered plasmids. ... Restriction sites, or restriction recognition sites, are particular sequences of nucleotides that are recognized by restriction enzymes as sites to cut the DNA molecule. ... It has been suggested that this article or section be merged into Transfection. ... Lysis (Greek lusis from luein = to separate) is the reduction of symptoms of a disease the dissolving of cells osmotic lysis chemical lysis viral lysis a dialogue of Plato about friendship (philia) This is a disambiguation page — a navigational aid which lists other pages that might otherwise share the same... This article is considered orphaned, since there are very few or no other articles that link to this one. ...


Another major use of plasmids is to make large amounts of proteins. In this case, researchers grow bacteria containing a plasmid harboring the gene of interest. Just as the bacteria produces proteins to confer its antibiotic resistance, it can also be induced to produce large amounts of proteins from the inserted gene. This is a cheap and easy way of mass-producing a gene or the protein it then codes for, for example, insulin or even antibiotics. Not to be confused with inulin. ... Staphylococcus aureus - Antibiotics test plate. ...


However, a plasmid can only contain inserts of about 1-10 kbp. To clone longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids, bacterial artificial chromosomes or yeast artificial chromosomes could be used. Base pairs, of a DNA molecule. ... Enterobacteria phage λ (lambda phage) is a temperate bacteriophage that infects Escherichia coli. ... A cosmid is a type of plasmid (often used as a cloning vector) constructed by the insertion of cos sequences, DNA-Sequences of the Phage Lambda Virus. ... A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. ... A yeast artificial chromosome (short YAC) is a vector used to clone large DNA fragments (larger than 100 kb and up to 3000 kb). ...


Types

Figure 4: Overview of Bacterial conjugation

One way of grouping plasmids is by their ability to transfer to other bacteria. Conjugative plasmids contain so-called tra-genes, which perform the complex process of conjugation, the transfer of plasmids to another bacterium (Fig. 4). Non-conjugative plasmids are incapable of initiating conjugation, hence they can only be transferred with the assistance of conjugative plasmids, by 'accident'. An intermediate class of plasmids are mobilizable, and carry only a subset of the genes required for transfer. They can 'parasitise' a conjugative plasmid, transferring at high frequency only in its presence. Plasmids are now being used to manipulate DNA and may possibly be a tool for curing many diseases. Image File history File links Download high-resolution version (694x813, 61 KB) Original work by Mike Jones for Wikipedia Overview of bacterial conjugation in 4 steps File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Image File history File links Download high-resolution version (694x813, 61 KB) Original work by Mike Jones for Wikipedia Overview of bacterial conjugation in 4 steps File history Legend: (cur) = this is the current file, (del) = delete this old version, (rev) = revert to this old version. ... Bacterial conjugation is the transfer of genetic material between bacteria through direct cell-to-cell contact. ...


It is possible for plasmids of different types to coexist in a single cell. Seven different plasmids have been found in E. coli. But related plasmids are often incompatible, in the sense that only one of them survives in the cell line, due to the regulation of vital plasmid functions. Therefore, plasmids can be assigned into compatibility groups. See also Entamoeba coli. ...


Another way to classify plasmids is by function. There are five main classes:

  • Fertility-F-plasmids, which contain tra-genes. They are capable of conjugation.
  • Resistance-(R)plasmids, which contain genes that can build a resistance against antibiotics or poisons. Historically known as R-factors, before the nature of plasmids was understood.
  • Col-plasmids, which contain genes that code for (determine the production of) bacteriocins, proteins that can kill other bacteria.
  • Degradative plasmids, which enable the digestion of unusual substances, e.g., toluene or salicylic acid.
  • Virulence plasmids, which turn the bacterium into a pathogen.

Plasmids can belong to more than one of these functional groups. To meet Wikipedias quality standards, this article or section may require cleanup. ... Bacterial conjugation is the transfer of genetic material between bacteria through direct cell-to-cell contact. ... Staphylococcus aureus - Antibiotics test plate. ... For other uses, see Poison (disambiguation). ... Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar bacterial strain(s). ... A representation of the 3D structure of myoglobin showing coloured alpha helices. ... Toluene, also known as methylbenzene or phenylmethane is a clear, water-insoluble liquid with the typical smell of paint thinners, redolent of the sweet smell of the related compound benzene. ... Salicylic acid (from the Latin word for the willow tree, Salix, from whose bark it can be obtained) is a beta hydroxy acid (BHA) with the formula C6H4(OH)CO2H, where the OH group is adjacent to the carboxyl group. ... A pathogen (from Greek pathos, suffering/emotion, and gene, to give birth to), infectious agent, or more commonly germ, is a biological agent that causes disease or illness to its host. ...


Plasmids that exist only as one or a few copies in each bacterium are, upon cell division, in danger of being lost in one of the segregating bacteria. Such single-copy plasmids have systems which attempt to actively distribute a copy to both daughter cells. This does not adequately cite its references or sources. ...


Some plasmids include an addiction system or "postsegregational killing system (PSK)", such as the hok/sok (host killing/suppressor of killing) system of plasmid R1 in Escherichia coli.[3] They produce both a long-lived poison and a short-lived antidote. Daughter cells that retain a copy of the plasmid survive, while a daughter cell that fails to inherit the plasmid dies or suffers a reduced growth-rate because of the lingering poison from the parent cell. The host killing/supressor of killing system, also known as hok/sok system, in molecular biology, is a postsegregational killing system of the plasmid R1 of Escherichia coli. ... E. coli redirects here. ... For other uses, see Poison (disambiguation). ... An antidote is a substance which can counteract a form of poisoning. ...


Plasmid DNA extraction

As alluded to above, plasmids are often used to purify a specific sequence, since they can easily be purified away from the rest of the genome. For their use as vectors, and for molecular cloning, plasmids often need to be isolated. For the cloning of human beings, see human cloning. ...


There are several methods to isolate plasmid DNA from bacteria, the archetypes of which are the miniprep and the maxiprep/bulkprep.[2] The former can be used to quickly find out whether the plasmid is correct in any of several bacterial clones. The yield is a small amount of impure plasmid DNA, which is sufficient for analysis by restriction digest and for some cloning techniques. A restriction digest is a molecular biology procedure used to prepare DNA for analysis or other processing. ...


In the latter, much larger volumes of bacterial suspension are grown from which a maxi-prep can be performed. Essentially this is a scaled-up miniprep followed by additional purification. This results in relatively large amounts (several micrograms) of very pure plasmid DNA.


In recent times many commercial kits have been created to perform plasmid extraction at various scales, purity and levels of automation. Commercial services can prepare plasmid DNA at quoted prices below $300/mg in milligram quantities and $15/mg in gram quantities (early 2007). 2007 is a common year starting on Monday of the Gregorian calendar. ...


Conformations

Plasmid DNA may appear in one of five conformations, which (for a given size) run at different speeds in a gel during electrophoresis. The conformations are listed below in order of electrophoretic mobility (speed for a given applied voltage) from slowest to fastest: For specific types of electrophoresis (for example, the process of administering medicine, iontophoresis), see electrophoresis (disambiguation). ...

  • "Nicked Open-Circular" DNA has one strand cut.
  • "Relaxed Circular" DNA is fully intact with both strands uncut, but has been enzymatically "relaxed" (supercoils removed). You can model this by letting a twisted extension cord unwind and relax and then plugging it into itself.
  • "Linear" DNA has free ends, either because both strands have been cut, or because the DNA was linear in vivo. You can model this with an electrical extension cord that is not plugged into itself.
  • "Supercoiled" (or "Covalently Closed-Circular") DNA is fully intact with both strands uncut, and with a twist built in, resulting in a compact form. You can model this by twisting an extension cord and then plugging it into itself.
  • "Supercoiled Denatured" DNA is like supercoiled DNA, but has unpaired regions that make it slightly less compact; this can result from excessive alkalinity during plasmid preparation. You can model this by twisting a badly frayed extension cord and then plugging it into itself.

The rate of migration for small linear fragments is directly proportional to the voltage applied at low voltages. At higher voltages, larger fragments migrate at continually increasing yet different rates. Therefore the resolution of a gel decreases with increased voltage. Supercoiled structure of circular DNA molecules with low writhe. ... The capitalization of this page is due to be corrected to Extension cord. ... Irreversible egg protein denaturation and loss of solubility, caused by the high temperature (while cooking it) Denaturation is the alteration of a protein or nucleic acids shape through some form of external stress (for example, by applying heat, acid or alkali), in such a way that it will no...


At a specified, low voltage, the migration rate of small linear DNA fragments is a function of their length. Large linear fragments (over 20kb or so) migrate at a certain fixed rate regardless of length. This is because the molecules 'reptate', with the bulk of the molecule following the leading end through the gel matrix. Restriction digests are frequently used to analyse purified plasmids. These enzymes specifically break the DNA at certain short sequences. The resulting linear fragments form 'bands' after gel electrophoresis. It is possible to purify certain fragments by cutting the bands out of the gel and dissolving the gel to release the DNA fragments. A restriction digest is a molecular biology procedure used to prepare DNA for analysis or other processing. ... Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid, ribonucleic acid, or protein molecules using an electric current applied to a gel matrix. ...


Because of its tight conformation, supercoiled DNA migrates faster through a gel than linear or open-circular DNA.


Simulation of plasmids

The use of plasmids as a technique in molecular biology is supported by bioinformatics software. These programmes record the DNA sequence of plasmid vectors, help to predict cut sites of restriction enzymes, and to plan manipulations. Examples of software packages that handle plasmid maps are Lasergene, GeneConstructionKit, and Vector NTI. Map of the human X chromosome (from the NCBI website). ... Computer software (or simply software) refers to one or more computer programs and data held in the storage of a computer for some purpose. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the phosphate backbones of the double helix without damaging the bases. ...


See also

A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. ... 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. ... A DNA composite transposon. ... An artists rendering of an Enterobacteria phage T4. ... A provirus is a retrovirus that has integrated itself into the DNA of a host cell. ...

References

  • Klein, Donald W.; Prescott, Lansing M.; Harley, John (1999). Microbiology. Boston: WCB/McGraw-Hill. 
  • Smith, Christopher U. M.. Elements of Molecular Nerobiology. Wiley, 101,111. 
  1. ^ LEDERBERG J (1952). "Cell genetics and hereditary symbiosis". Physiol. Rev. 32 (4): 403-30. 
  2. ^ a b Russell, David W.; Sambrook, Joseph (2001). Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory. 
  3. ^ Gerdes K, Rasmussen PB, Molin S (1986). "Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells". Proc. Natl. Acad. Sci. U.S.A. 83 (10). 

External links

  • International Society for Plasmid Biology and other Mobile Genetic Elements
  • History of Plasmids with timeline

Episomes

  • Overview: viral and non-viral episomes
  • Replicating minicircles: novel non-viral episomes


  Results from FactBites:
 
Plasmid Insertion (217 words)
Process by which a plasmid is used to import recombinant DNA into a host cell for cloning.
The plasmid is opened up and the gene is freed from its parent DNA strand.
They have complementary "sticky ends." The opened plasmid and the freed gene are mixed with DNA ligase, which reforms the two pieces as recombinant DNA.
  More results at FactBites »

 
 

COMMENTARY     


Share your thoughts, questions and commentary here
Your name
Your comments

Want to know more?
Search encyclopedia, statistics and forums:

 


Press Releases |  Feeds | Contact
The Wikipedia article included on this page is licensed under the GFDL.
Images may be subject to relevant owners' copyright.
All other elements are (c) copyright NationMaster.com 2003-5. All Rights Reserved.
Usage implies agreement with terms, 1022, m