Plasmid

On the basis of need of specific content of any topic, i prepared a slides of plasmid for needy students. I'm also a student that's why i know how useful a proper presentation for us.
In this presentation, i try to cover some basic knowledge regarding to plasmid. If you like this ppt than please let me know, it gives me a motivation. If you need other topics ppt then write a topic name on comment section. THANK YOU

1. B.S.A. College PLASMID By- Arti Singh

2. Content Introduction What is Plasmid? Structure of Plasmid Plasmid Elements General properties of Plasmid Replication in Plasmid General types of Plasmid Specific types of Plasmid Other types of Plasmid Applications of Plasmid

3. Introduction The very existence of plasmids in bacterial cytoplasm was revealed by Lederberg in 1952 while working on conjugation process in bacteria. Lederberg coined the term ‘ Plasmid ’ to refer to the transmissible genetic elements that were transferred from one bacterial cell to another and determined the maleness in bacteria. Literally, thousands of plasmids are now known; over 300 different naturally occurring plasmids have been isolated from strains of Escherichia coli alone.

4. What is Plasmid? A plasmid is a small, circular piece of DNA that is different than the chromosomal DNA. They are capable of replicating independently. As such, they do not rely on chromosomal DNA of the organism for replication. Because of this characteristic, they are also referred to as Extra-Chromosomal DNA. Plasmids are mainly found in bacteria. Plasmids usually carry at least one gene and many of the genes that plasmids carry are beneficial to their host organisms. Although they have separate genes from their hosts, they are not considered to be independent life.

5. General properties of Plasmid They are specific to one or a few particular bacteria. They replicate independently of the bacterial chromosome. They code for their own transfer. They act as episomes and reversibly integrate into bacterial chromosome. They may pick-up and transfer certain genes of bacterial chromosome. They may affect certain characteristics of the bacterial cell. Plasmids differ from viruses in following two ways- They do not cause damage to cells and generally are beneficial. They do not have extracellular forms and exist inside cells simply as free and typically circular DNA.

6. Replication in Plasmid DNA There are three types of plasmid replication- 1. Rolling circle :  Rolling circle replication mechanism is specific to bacteriophage family m13 and the fertility F factor which encodes for sex pili formation during recombination by means of conjugation. Fragments smaller than 10 kilo base usually replicate by this replication mechanism as reported in some gram positive bacteria. It allows the transfer of single stranded replication product at a faster rate to the recipient cell through pilus as in case of fertility factor or to the membrane in case of phage.

7. 2. Col E1 type replication :   Col E1 replication is a negative regulation mechanism which enables the plasmid to control its own copy numbers by involving RNA type I, RNA type II, Rom protein, and the plasmid itself. Col E1 replication is initiated by means of RNA-RNA interactions and does not rely on replication initiation protein encoded by the plasmid to regulate its copy number. 

8. 3. Iteron -containing replicons :  This replicon consists of a gene that encodes Rep protein for plasmid replication initiation, set of direct repeat sequences called iteron , adjacent AT-rich region and Dna boxes which is a protein required for bacterial chromosome replication initiation. However length of adjacent AT-rich region and number of iterons and DnaA boxes differs in a replicon .

9. General types of Plasmid Conjugative and Non-Conjugative One way is by grouping them as either conjugative or non-conjugative. Bacteria reproduce by sexual conjugation, which is the transfer of genetic material from one bacterial cell to another, either through direct contact or a bridge between the two cells. Some plasmids contain genes called transfer genes that facilitate the beginning of conjugation. Non-conjugative plasmids cannot start the conjugation process, and they can only be transferred through sexual conjugation with the help of conjugative plasmids. Incompatibility Another plasmid classification is by incompatibility group. In a bacterium, different plasmids can only co-occur if they are compatible with each other. An incompatible plasmid will be expelled from the bacterial cell. Plasmids are incompatible if they have the same reproduction strategy in the cell; this allows the plasmids to inhabit a certain territory within it without other plasmids interfering.

10. Specific types of Plasmid There are five main types of plasmids: 1.Fertility Plasmids also known as F-plasmids , contain transfer genes that allow genes to be transferred from one bacteria to another through conjugation. These make up the broad category of conjugative plasmids. F-plasmids are episomes , which are plasmids that can be inserted into chromosomal DNA. Bacteria that have the F-plasmid are known as F positive (F + ), and bacteria without it are F negative (F – ). When an F +  bacterium conjugates with an F –  bacterium, two F +  bacterium result. There can only be one F-plasmid in each bacterium 2.Resistance Plasmids or R plasmids contain genes that help a bacterial cell defend against environmental factors such as poisons or antibiotics. Some resistance plasmids can transfer themselves through conjugation. When this happens, a strain of bacteria can become resistant to antibiotics.  

11. 3.Virulence Plasmids when a virulence plasmid is inside a bacterium, it turns that bacterium into a pathogen, which is an agent of disease. Bacteria that cause disease can be easily spread and replicated among affected individuals. The bacterium  Escherichia coli (E. coli)  has several virulence plasmids.  E. coli  is found naturally in the human gut and in other animals, but certain strains of  E. coli  can cause severe diarrhea and vomiting.  Salmonella enterica  is another bacterium that contains virulence plasmids. 4.Degradative plasmids help the host bacterium  to digest compounds that are not commonly found in nature, such as camphor, xylene , toluene, and salicylic acid. These plasmids contain genes for special enzymes that break down specific compounds. Degradative plasmids are conjugative. 5.Col plasmids contain genes that make bacteriocins (also known as colicins ), which are proteins that kill other bacteria and thus defend the host bacterium. Bacteriocins are found in many types of bacteria including  E. coli , which gets them from the plasmid ColE1.

12. Other types of Plasmid Plasmids are versatile and can be used in many different ways by scientists. Cloning Plasmids   - Used to facilitate the cloning of DNA fragments. Cloning vectors tend to be very simple, often containing only a bacterial resistance gene, origin of replication, and MCS. They are small and optimized to help in the initial cloning of a DNA fragment. Commonly used cloning vectors include Gateway entry vectors and TOPO cloning vectors.  Expression Plasmids  - Used for gene expression (for the purposes of gene study). Expression vectors must contain a promoter sequence, a transcription terminator sequence, and the inserted gene. The promoter region is required for the generation of RNA from the insert DNA via transcription. The terminator sequence on the newly synthesized RNA signals for the transcription process to stop. An expression vector can also include an enhancer sequence which increases the amount of protein or RNA produced. Expression vectors can drive expression in various cell types (mammalian, yeast, bacterial, etc.), depending largely on which promoter is used to initiate transcription.

13. Gene Knock-down Plasmids   - Used for reducing the expression of an endogenous gene. This is frequently accomplished through expression of an shRNA targeting the mRNA of the gene of interest. These plasmids have promoters that can drive expression of short RNAs. Genome Engineering Plasmids  - Used to target and edit genomes. Genome editing is most commonly accomplished using CRISPR technology. CRISPR is composed of a DNA endonuclease and guide RNAs that target specific locations in the genome. Reporter Plasmids  - Used for studying the function of genetic elements. These plasmids contain a reporter gene (for example, luciferase or GFP) that offers a read-out of the activity of the genetic element. For instance, a promoter of interest could be inserted upstream of the luciferase gene to determine the level of transcription driven by that promoter.

14. Viral Plasmids  - These plasmids are modified viral genomes that are used to efficiently deliver genetic material into target cells. You can use these plasmids to create viral particles, such as lentiviral , retroviral, AAV, or adenoviral particles, that can infect your target cells at a high efficiency. 

15. Applications of Plasmid Humans have developed many uses for plasmids and have created software to record the DNA sequences of plasmids for use in many different techniques.  Plasmids are used in genetic engineering to amplify, or produce many copies of, certain genes. A vector is a DNA sequence that can transport foreign genetic material from one cell to another cell, where the genes can be further expressed and replicated. Plasmids are useful in cloning short segments of DNA. Also, plasmids can be used to replicate proteins, such as the protein that codes for  insulin , in large amounts. Additionally, plasmids are being investigated as a way to transfer genes into human cells as part of gene therapy . Cells may lack a specific protein if the patient has a hereditary disorder involving a gene mutation . Inserting a plasmid into DNA would allow cells to express a protein that they are lacking. In nature, plasmids often carry genes that benefit the survival of the organism, such as by providing  antibiotic resistance.

16.   Artificial plasmids are widely used as  vectors  in molecular cloning, serving to drive the replication of  recombinant DNA sequences within host organisms. Plasmids are considered  replicons , units of DNA capable of replicating autonomously within a suitable host. This host-to-host transfer of genetic material is one mechanism of  horizontal gene transfer , and plasmids are considered part of the  mobilome . Unlike viruses, which encase their genetic material in a protective protein coat called a  capsid , plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host. However, some classes of plasmids encode the  conjugative "sex" pilus  necessary for their own transfer. The size of the plasmid varies from 1 to over 200 kbp ,  and the number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances. The relationship between microbes and plasmid DNA is neither parasitic nor mutualistic , because each impliesthe presence of an independent species living in a detrimental or commensal state with the host organism. Plasmids can also provide bacteria with the ability to  fix nitrogen .