Formation of low mass protostars and their circumstellar disks
Vectors Used for Gene Cloning in Plants
1. VECTORS USED FOR
GENE CLONING IN
PLANTS
Submitted By :
Arunodaya Maji
CARA-2018-110
Batch - D
Submitted To :
Dr. G. Uma Devi Ma’am
College of Agriculture, Rajendranagar
Course No. – PATH – 271
Course Title – Principles of Plant Pathology
Course Credits – 2(2+0)
Assignment - 3
2. Content
1. What is cloning vector ?
2. Why cloning vector ?
3. History
4. What determines choice of vector
5. Features of a cloning vector
6. Types of cloning vector
7. Agrobacterium Mediated Cloning Vectors
Ti Plasmid
Ri Plasmid
8. Attempts to use Plant Viruses as Cloning Vectors
9. Conclusion
10. References
3. Cloning Vectors
The molecular analysis of DNA has been made possible by the cloning of DNA.
The two molecules that are required for cloning are the DNA to be cloned and a
cloning vector.
A cloning vector is a small piece of DNA taken from a virus, a plasmid or the
cell of a higher organism, that can be stably maintained in an organism and
into which a foreign DNA fragment can be inserted for cloning purposes.
Most vectors are genetically engineered.
The cloning vector is chosen according to the size and type of DNA to be cloned.
The vector therefore contains features that allow for the convenient insertion or
removal of DNA fragment in or out of the vector, for example by treating the
vector and the foreign DNA with a restriction enzyme and then ligating the
fragments together.
After a DNA fragment has been cloned into a cloning vector, it may be further
subcloned into another vector designed for more specific use.
4. Vector
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.
5. Why Cloning Vectors
Cloning vector is used as a vehicle to artificially carry foreign genetic
material into another cell, where it can be replicated and expressed.
It is used to amplify a single molecule of DNA into many copes.
Cloning vectors are DNA molecules that are used to "transport" cloned
sequences between biological hosts and the test tube.
Without Cloning Vector, Molecular Gene Cloning is totally impossible.
6. History
Scientists (Herbert Boyer, Keiichi Itakura and Arthur Riggs) working in Boyer’s lab (University of
California) recognized a general cloning vector with unique restriction sites for cloning in foreign
DNA and the expression of antibiotic resistance genes for selection of transformed bacteria.
Rodriguez Raymon along with Paco Bolivar constructed the vector “pBR 322” in the year
1977
This vector was small, ~4 kb in size, and had two antibiotic resistance genes for selection.
Arthur Riggs Herbert BoyerRodriguez Raymon
7.
8. Features of A Cloning Vector
All commonly used cloning vectors have some essential features:
Origin of replication (ori):
This makes autonomous replication in vector.
ori is a specific sequence of nucleotide from where
replication starts.
When foreign DNA is linked to the sequence along with vector
replication, foreign (desirable) DNA also starts replicating within
host cell.
Cloning Site:
Cloning site is a place where the vector DNA can be digested and
desired DNA can be inserted by the same restriction enzyme.
It is a point of entry or analysis for genetic engineering work.
Recently recombinant plasmids contain a multiple cloning site
(MCS) which have many (up to ~20) restriction sites.
9. Selectable Marker
Selectable marker is a gene that confers resistance to particular antibiotics or selective
agent that would normally kill the host cell or prevent its growth.
A cloning vector contains a selectable marker, which confer on the host cell an ability to
survive and proliferate in a selective growth medium containing the particular antibiotics.
Reporter Gene or MarkerGene
Reporter genes are used in cloning vectors to facilitate the screening of successful clones by
using features of these genes that allow successful clone to be easily identified.
Such feature present in cloning vectors is used in blue- white selection.
10. Replicate autonomously.
Restriction sites.
Self replication, multiple copies.
Replication origin site.
Small size.(Larger plasmids are more difficult to characterize by restriction
mapping and replicate to lower copy numbers)
Low molecular weight.
No pathogenicity
Easily isolated & purified.
Easily isolated into host cell.
Control elements – promoter, operator, ribosome binding site.
13. Types Of Cloning Vectors
S. No. Vectors Targeted Host
1 Plasmid Bacteria, Streptomyces
2 Ti & Ri Plasmid Transformation of cloned genes
in Higher Plants
3 Bacteriophages/Phagemids/Phasmids Bacteria
4 Cosmid (Hybrid Vector) Bacteria
5 Fosmid E. coli
6 Bacterial Artificial Chromosome (BAC) Bacteria
7 Yeast Artificial Chromosome (YAC) Yeast
8 Human Artificial Chrosome (HAC) Human Cells
9 Mammalian Artificial Chromosome (MAC) Mammalian Cells
10 Shuttle Vectors E. coli, Yeast
11 Retroviral Vectors Human and Animal Cells
14. Agrobacterium Mediated Transformation
The important requirements for Agrobacterium- mediated gene
transfer in higher plants are as follows:-
The plant explants must produce acetosyringone for activation of
Vir genes.
The induced Agrobacterium should have access to cells that are
competent for transformation.
Explants include cotyledon, leaf, thin tissue layer, peduncle,
hypocotyls, stem, microspores
18. Agrobacterium tumifaciens
Agrobacterium tumefaciens—nature’s smallest genetic
engineer
A. tumefaciens causes CROWN GALL DISEASE in many
species of dicotyledonous plants.
Causes a cancerous proliferation of the stem tissue in the
region of the crown.
A. tumifaciens is a Gram –ve soil bacterium
Infects plants through breaks or wounds.
Tumor formation is the result of integration of T-DNA
(Transfer DNA) in plant genome.
21. Tzvi Tzfira and Vitaly Citovsky, 2002, Trends in Cell Biol. 12(3), 121-129
Cellular Processes of Agrobacterium Host Infection
22. In general, the transformation procedure is as follows:
The recombinant small replicon is transferred via bacterial conjugation or direct transfer to A. tumefaciens harboring a
helper Ti plasmid, the plant cells are co-cultivated with the Agrobacterium, to allow transfer of recombinant T-DNAin to the
plant genome, and transformed plant cells are selected under appropriate conditions.
1. Binary vector system involves only the transfer of a binary plasmid to Agrobacterium without any integration.
2. This is in contrast to co-integrate vector system wherein the intermediate vector is transferred and integrated with
disarmed Ti plasmid.
3. Due to convenience, binary vectors are more frequently used than co-integrate vectors.
Compared with co-integrated vectors, binary vectors present some advantages:
No recombination process takes place between the molecules involved.
Instead of a very large, recombinant, disarmed Ti plasmid, small vector s are used, which increases transfer
efficiency from E. coli to Agrobacterium.
This vector system is most widely used nowadays.
Different types of binary vectors have been devised to suit different needs in a plant transformation process.
25. Transformation Protocols
Transformation was performed using minor modifications of given protocols, using
I. Leaf disk
II. Scutellum-derived callus, or
III. Floral dip methods, respectively.
AGROBACTERIUM-MEDIATED PLANT TRANSFORMATIONS HAVE THE FOLLOWING BASIC
PROTOCOL :-
Development of Agrobacterium carrying the cointegrate or binary vector with the
desired gene.
Identification of a suitable explant e.g. cells, protoplasts, tissues, calluses, organs.
Co-culture of explants with Agrobacterium.
Killing of Agrobacterium with a suitable antibiotic without harming the plant tissue.
Selection of transformed plant cells.
Regeneration of whole plants.
26. Example-scutellum-derived callus method
Transformation Protocol for Rice – Abbreviated
Seed plating on 2N6 – dark
↓ 4 weeks Subculture onto 2N6 – dark
↓ 4 – 10 days
Co cultivation onto 2N6-AS – dark
↓ 3-7 days
Selection on 2N6-TCH – dark
↓ 4 weeks, subculture onto 2N6-TCH every 2 weeks Transfer proliferating calli onto 2N6-TCH-dark
↓ 2 weeks
Regeneration onto RGH6-dark
↓ 7 days Transfer to light
↓ 4-6 weeks Plantlets onto ½ MSH - light
↓
Transfer plants to the glasshouse
27. Seed Material: Oryza sativa L. ssp japonica cvs. Millin or Nipponbare.
Steps-
1. Callus Induction
2. Callus Subculture
3. Bacteria Preparation
4. Transformation
5. Callus washing
6. Selection
7. Regeneration
8. Plantlet Formation
To ensure that the gene transfer did not result from contamination with Agrobacterium cells, controls including species specific PCR,
selective plating, and use of atagged binary vector were implemented.
Thus, diverse plant associated bacteria, when harbouring a disarmed Ti plasmid and binary vector(or presumably a cointegrate or whole Ti
plasmid), are readily able to transfer TDNA to plants. The Ti plasmid is self transmissable, perhaps in dicating the existence of a ubiquitous
natural mechanism effecting horizontal gene transfer from bacteria to plants.
28. Procedure for Plant Transformation
IMAGE: Mol bio of the cell by Albert (pg no:599)
29. Regeneration, Selection And Detection
Regeneration: for shoot organogenesis, cytokinin (lower amounts of auxin) are required
Selection: two antibiotics are required
• An antibiotic to kill the Agrobacterium, while not affecting theplant's cell growth and
division
• a second antibiotic allows growth of transformed shoots (w/selectable
marker) but inhibits growth of untransformed plantcells.
Detection of the "trait" gene
PCR methods can detect the presence of the "trait" DNA
protein detection methods are used where a gene product is producedthat defines the trait
verification of the incorporation of the trait gene into the plant's chromosome:
• by Southern hybridization
• by demonstrating transfer of the trait to the originaltransformant's progeny.
30. Scientists can insert any gene they want into the plasmid in place of thetumor
causing genes and subsequently into the plant cell genome.
By varying experimental materials, culture conditions, bacterial strains, etc.
scientists have successfully used A. tumefaciens Gene Transfer to produce BT Corn.
This method of gene transfer enables large DNA strands to be transferred into the
plant cell without risk of rearrangement whereas other methods like the Gene Gun
have trouble doing this .
The vast majority of approved genetically engineered agriculture has been
transformed by means of Agrobacterium tumefaciens Mediated Gene Transfer.
Original problems existed in that Agrobacterium tumefaciens only affects
dicotyledonous plants.
Monocotyledon plants are not very susceptible to the bacterial infection.
Benefits and Problems with Agrobacteria
31. Ti Plasmid
The Ti plasmid (approx.size 200 kb each) exist as independent replicating
circular DNA molecules within the Agrobacterium cells.
The T-DNA is variable in length in the range of 12 to 24 kb.
The Ti plasmid is lost when Agrobacterium is grown above 28 °C.
The plasmid has 196 genes that code for 195 proteins. There is one structural
RNA. The plasmid is 206,479 nucleotides long, the GC content is 56% and
81% of the material is coding genes. There are no pseudogenes.
The modification of this plasmid is very important in the creation of
transgenic plants.
Genes in the virulence region are grouped into the operons virABCDEFG,
which code for the enzymes responsible for mediating conjugative transfer of
T-DNA to plant cells.
32. Though Ti plasmids are effective natural vectors they had certain limitations.
The phytohormone produced by transformed cells growing in culture
prevents their regeneration into mature plants. Hence auxins and cytokinin
genes must be removed from the Ti –plasmid derived cloning vector.
The opine synthesis gene must be removed as it m ay divert plant resources
into opine production in transgenic plant.
Generally, Ti- plasmids are large in size (200-800kb) For effective cloning,
large segments of DNA that are not essential for cloning has to be removed.
As Ti plasmid does not replicate in E.coli Ti-plasmid based vectors require an
ori that can be used in E.coli.
33. Binary vector
Plasmid DNA
VIR genes
Bacterial
ChromosomeBacterial ORI
t-DNA
Ampicillin
resistance
Construction of vector
with disired genes
34. To overcome these constraints, Ti plasmid based vectors were organized with the
following components:
A selectable marker gene that confers resistance to transformed plant cells. As these marker genes
are prokaryotic origin, it is necessary to put them under the eukaryotic control (plant) of post
transcriptional regul ation signals, including promoter and a termination- poly adenylation
sequence, to ensure that it is efficiently expressed in transformed plant cells.
An origin of replication that allows the plasmid to replicate in E.coli.
The right border sequence of the T-DNA which is necessary for T- DNA integration into plant cell
DNA.
A polylinker (MCS) to facilitate the insertion of cloned gene into the region between T-DNA
border sequences.
37. 1. T-DNA Region :This region has the genes for the Biosynthesis
of Auxin (aux), Cytokinin (cyt), and Opine (ocs)
T-DNA Border : A set of 24 bp sequence present on either side of T-DNA
2. Virulence Region : The genes responsible for the transfer of T-
DNA into the host plant are located outside the T-
DNA ant the region referred to as vir or virulence
region
3. Opine Catabolism region : Uptake and Metabolism of Opine
Organization of Ti-Plasmid
A B C D E G
39. virA- Transports acetosyringone into bacterium, activates virG post-
translationally (by phosphorylation)
virG - Promotes transcription of other vir genes
virD2- Endonuclease/integrase that cuts T-DNA at the borders but only on one
strand.
virE2 - Can form channels in membranes
virE1 - Chaperone for virE2
virD2 & virE2 also have NLSs, gets T-DNA to the nucleus of plant cell
virB - Operon of 11 proteins, gets T-DNA through bacterial membranes
Function of Vir genes
40. Opines
Derivatives of amino acids synthesized by T-DNA.
Ti plasmids can be classified according to the opines produced :
1. Nopaline plasmids
2. Octopine plasmids
3. Agropine plasmids
Nopaline plasmids : carry gene for synthesizing nopaline in the plant
and for utilization (catabolism) in the bacteria.
Octopine plasmids : carry genes to synthesize octopine in the plant
and catabolism in the bacteria.
Agropine plasmids : carry genes for agropine synthesis and
catabolism.
42. 1. Signal Induction : Wounded Plant cells release certain phenolic compounds which
are recognized as signals by agrobacterium.
Wound Phenolic compounds Signal
2. Attachment : The Agrobacterium attaches to palnt cells through polysaccharides, particularly via
cellulosefibers
Plant CellBacteria
Vir G VirB,C,D,E
3. Production of Virulance Proteins :
Signal Vir A
Vir A
43. 4. Production of T-DNA Strand : The right and left border of T-DNA are recognized by
D1/D2 proteins and these proteins involved in the
production of ss-DNA.
5. Transfer of T-DNA out of Agrobacterium : Vir B form transport apparatus and ss-T-
DNA in association with vir D2 exported from the
bacterial cell.
6. Transfer of T-DNA into plant cells and its Integration : In plant cell ss T-DNA get
covered with vir E2 for its protection. Vir D2 and E2 interact
with variety of plants proteins which influences T-DNA transport
and its integration into plant genome. (illegitimate
Recombination)
Transcription Translation Crown GallIntegration
44. B
B
A
G
D
2
D
2
D1/D2
D1/D2
B C D E
E2
SS-T DNA
Wounded Plant cell
E2
T
i
1
2
3 4
5 6
Transcription
Translation
Production of
auxin, cytokinin
and opine
Autostimulation of
Cell division
Bacteria
45. Making of Co-Integrate Vectors
In this strategy, both the T-DNA with our gene of interest and vir region are present in the
same vector used for transformation.
At first; an intermediate vector is made using E.coli plasmid + vir region + T-DNA borders +
origin of replication+pBR 322 sequences.
Second vector is a disarmed pTi vector = gene of interest+ some markers+pBR322 sequences.
Both intermediate vector and disarmed pTi has some sequences in common (pBR322
sequences).
Therefore by homologous recombination, co-integration of two plasmids will take place within
Agrobacterium.
Now we have a co-integrate vector that has both T-DNA with our gene of interest with in the T-
DNA borders and vir region. This complete vector is used for transformation eg:pGV2260.
There are two types of Ti plasmid vectors are used for genetic transformation of plant
they are cointegrate vector and binary vector.
47. Advantages of Co-integrate Vector
Target genes can be easily cloned.
The plasmid is relatively small with a number of restriction
sites.
Intermediate plasmid is convenientiy cloned in E.coli and
transferred to Agrobacterium.
48. Binary vector strategy: Two vector strategy
Here two vectors are used. This vector was devised based on the knowledge that vir region need not be in the
same plasmid along with T-DNA for T DNA transfer.
Binary vector consists of a pair of plasmids
1) A disarmed Ti plsmid: This plasmid has T-DNA with gene of interest + ori for both E.coli and
Agrobacterium. Also called as mini-Ti or micro Ti plasmid eg: Bin 19
2) Helper Ti plasmid has virulence region that mediates transfer of T-DNA in micro Ti plasmid to the
plant.
49. The binary vector system consist of an Agrobacterium strain along with a disarmed Ti plasmid called vir helper plasmid
(the entire T-DNA region including borders deleted while vir gene is retained). It may be noted that both of them are not
physically linked (or integrated). A binary vector with T-DNA can replicate in E.coli and Agrobacterium.
The binary vector has following components-:
1. Left and right borders that delimit the T-DNA region.
2. A plant transformation marker (PTM) e.g. npt2 that confers kanamycin resistance in plant transformed cells.
3. A multiple cloning site (MCS) for introducing target/foreign genes.
4. A bacterial resistance marker e.g. tetracycline resistance gene for selecting binary vector colonies in E.coli and
Agrobacterium.
5. Ori T sequence for conjugal mobilization of the binary vector from E.coli to Agrobacterium.
6. A broad host- range origin of replication such as RK2 that allows the replication of binary vector in Agrobacterium.
The target (foreign) gene of interest is inserted into the multiple cloning site of the binary vector.
In this way, the target gene is placed between the right and left border repeats and cloned in E.coli.
By a mating process, the binary vector is mobilised from E.coli to Agrobacterium.
Now, the virulence gene proteins of T-DNA of the vector into plant cells.
The binary vector system involves only the transfer of a binary plasmid to Agrobacterium without any
integration.
This is in contrast to cointegrate vector system wherein the intermediate vector is transferred and integrated
with disarmed Ti plasmid.
Due to convenience, binary vectors are more frequently used than cointegrate vectors.
50. Limitations of Ti – Plasmid
LARGE SIZE.
TUMOR INDUCTION PROPERTY.
ABSENCE OF UNIQUE RESTRICTION SITES.
51.
52. Ri Plasmid
The virulence plasmid of A. rhizogenes is commonly known as Ri- Plasmid (pRi).
Agrobacterium rhizogene is a soil borne , gram negative bacterium.
All strains of A. rhizogenes are known to produce agrocinopine.
Causes hairy root disease, i.e., massive proliferation of a highly branched root system.
This is used for obtaining large amounts of protein from genes cloned in plants
Ri plasmids are large (200 to greater than 800 kb) .
Contain one or two regions of T-DNA and a vir (virulence) region, all of which are necessary
for hairy root formation.
The Ri-plasmids are grouped into two main classes according to the opines synthesized by
hairy roots.
First, agropine-type strains induce roots to synthesise agropine, mannopine and the related
acids.
Second, mannopine-type strains induce roots to produce mannopine and the corresponding
acids.
55. D
D
irect gene transfer by precipitation of
NA onto the surfaces of protoplasts.
Direct gene transfer.
56. Limitations of cloning with Agrobacterium plasmids
Extensively used in dicots, but much more difficult to obtain the same
results with monocots.
But yet eventually artificial techniques for achieving T-DNA transfer
in monocots were devised.
Ease of recovery of plants varies with species.
Hence gene gun technique is being used
57. ATTEMPTS TO USE PLANT VIRUSES AS CLONING VECTORS
The potential of plant viruses as cloning vectors has been explored for several years, but without great success.
One problem here is that the vast majority of plant viruses have genomes not of DNA but of RNA. RNA viruses
are less useful as potential cloning vectors because manipulations with RNA are more difficult to carry out. Only
two classes of DNA virus are known to infect higher plants – the caulimoviruses and geminiviruses – and
neither is ideally suited to gene cloning.
Caulimovirus vectors
Although one of the first successful plant genetic engineering experiments, performed back in 1984, used a
caulimovirus vector to clone a new gene into turnip plants, two general difficulties with these viruses have
limited their usefulness.
59. The first problem is that the total size of a caulimovirus genome is, like that of λ, constrained by the need
to package it into its protein coat.
Even after the deletion of non-essential sections of the virus genome the capacity for carrying inserted DNA
is still very limited.
Recent studies have shown that it might be possible to circumvent this problem by adopting a helper virus
strategy, similar to that used with phagemids .
In this strategy, the cloning vector is a cauliflower mosaic virus (CaMV) genome that lacks several of the
essential genes, which means that it can carry a large DNA insert but cannot, by itself, direct infection.
60. Plants are inoculated with the vector DNA along with a normal CaMV genome.
The normal viral genome then provides the genes needed for the cloning vector to be packaged into virus
proteins and spread through the plant.
Although this approach has considerable potential it does not solve the second problem, which is the
extremely narrow host range of caulimoviruses.
This restricts cloning experiments to just a few plants, mainly brassicas such as turnips, cabbages and
cauliflowers.
Caulimoviruses have, however, been important in genetic engineering as the source of highly active
promoters that function in all plants and that are used to obtain expression of genes introduced by Ti plasmid
cloning or direct gene transfer.
61. Geminivirus Vectors
The geminiviruses are particularly interesting because their natural hosts include plants such as maize and
wheat, and they could therefore serve as potential vectors for these and other monocots.
But geminiviruses have presented their own set of difficulties, one problem being that during the infection
cycle the genomes of some geminiviruses undergo rearrangements and deletions, which would scramble up
any additional DNA that has been inserted – an obvious disadvantage for a cloning vector.
Investigations performed over the years have addressed these problems and geminiviruses are now
beginning to find some specialist applications in plant gene cloning.
One such application is virus-induced gene silencing (VIGS), a technique used to investigate the functions
of individual plant genes.
62.
63. The use of a geminivirus vector to silence a
plant gene via virus-induced gene silencing.
• This method exploits one of the natural defence
mechanisms that plants use to protect themselves
against viral attack.
• This method, termed RNA silencing, results in the
degradation of viral mRNAs.
• If one of the viral RNAs is transcribed from a cloned
gene contained within a geminivirus genome, then not
only are the viral transcripts degraded but also the
cellular mRNAs derived from the plant’s copy of the
gene . Consequently, the plant gene becomes silenced
and the effect of its inactivation on the phenotype of the
plant can be studied.
64. Genome maps of (a) African cassava mosaic virus (ACMV)
and (b) maize streak virus (MSV), representative of the
majority of dicot- and monocot-infecting geminiviruses,
respectively. Coding regions are referred to as virion-sense
(V) and complementary-sense (C) depending on their
orientation relative to the virion ssDNA. ACMV AVI and MSV
V2 encode coat proteins. ACMV AC1 and the MSV C1-C2
fusion protein are essential for viral-DNA replication, while
ACMV BVl and BCI, and MSV Vl participate in virus spread.
ACMV AC2 trans-activates coat-protein expression and AC3
is required for efficient viral-DNA replication. The functions
of ACMV AV2 and AC4 are unknown. Intergenic sequences
conserved between ACMV DNA A and DNA B (dark shading)
contain c/s-acting elements that participate in DNA replication
and the control of bidirectional gene expression. Positions of
the large intergenic region (LIR) and small intergenic region
(SIR) of MSV are indicated. Sequences that are dispensible
for viral-DNA replication are light-shaded; the ACMV
sequences are also dispensible for systemic infection of
Nicotiana benthamiana.
65. References
1. www.asgct.org › General Public › Educational Resources
2. www.link.springer.com
3. www.bios.net
4. Wikipedia
5. http://nptel.ac.in/courses/102103016/module3/lec23/2.html
6. Plant biotechnology – the genetic manipulations of plants 2nd edition by Adrian Slater, Nigel W.Scott & Mark R. Fowler
7. Principles of gene Manipulations & Genomics – Primrose & Twyman 7th edition
8. Joseph Sambrook, David Russell. "Chapter 1". Molecular Cloning – A Laboratory Manual 1 (3rd ed.)
9. https://www.ndsu.edu/pubweb/~mcclean/plsc431/cloning/clone3.htm
10. http://www.chemistrylearning.com/cloning-vector/
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