In this section we are deals with BIOTECHNOLOGY PRINCIPLES PROCESSES CHAPTER11 of biology.Important points,notes,pdf,questions are included
11.1 PRINCIPLES OF BIOTECHNOLOGY
Among many, the two core techniques that enabled birth
of modern biotechnology are :
(i) Genetic engineering : Techniques to alter the chemistry of genetic material (DNA and RNA),to introduce these into host organisms and thus change the phenotype of the host organism.
(ii) Bioprocess engineering: Maintenance of sterile (microbial contamination-free) ambience in chemical engineering processes
to enable growth of only the desired microbe/eukaryotic cell in large quantities for the manufacture of biotechnological products like antibiotics, vaccines, enzymes, etc.
Traditional hybridisation procedures used in plant and
animal breeding, very often lead to inclusion and multiplication of undesirable genes along with the desired genes. The techniques of genetic engineering which include creation of recombinant DNA, use of gene cloning and gene transfer, overcome this limitation and allows us
to isolate and introduce only one or a set of desirable genes without introducing undesirable genes into the target organism.
Most likely, this piece of DNA would not be able to multiply itself in the progeny cells of the organism. But, when it gets integrated into the genome of the recipient, it may multiply and be inherited along with the host DNA. This is because the alien piece of DNA has become part of a chromosome, which has the ability to replicate. In a chromosome there is a specific DNA sequence called the origin of replication, which is responsible for initiating replication. Therefore, for the multiplication of any alien piece of DNA in an organism it needs to be a part of a chromosome(s) which has a specific sequence known as ‘origin of replication’. Thus, an alien DNA is linked with the origin of replication, so that, this alien piece of DNA can replicate and
multiply itself in the host organism. This can also be called as cloning or
making multiple identical copies of any template DNA.
The construction of the first recombinant DNA emerged from the possibility of linking a gene encoding antibiotic resistance with a native plasmid (autonomously replicating circular extra-chromosomal DNA) of Salmonella typhimurium. Stanley Cohen and Herbert Boyer accomplished this in 1972 by isolating the antibiotic resistance gene by cutting out a piece of DNA from a plasmid which was responsible for conferring antibiotic resistance. The cutting of DNA at specific locations became possible with the discovery of the so-called ‘molecular scissors’– restriction enzymes. The cut piece of DNA was then linked with the plasmid DNA. These plasmid DNA act as vectors to transfer the piece of DNA attached to it. You probably know that mosquito acts as an insect vector to transfer the malarial parasite into human body.
In the same way, a plasmid can be used as vector to deliver an alien piece
of DNA into the host organism. The linking of antibiotic resistance gene
with the plasmid vector became possible with the enzyme DNA ligase, which acts on cut DNA molecules and joins their ends. This makes a new combination of circular autonomously replicating DNA created in vitro
and is known as recombinant DNA. When this DNA is transferred into
Escherichia coli, a bacterium closely related to Salmonella, it could replicate using the new host’s DNA polymerase enzyme and make multiple copies. The ability to multiply copies of antibiotic resistance gene in
E. coli was called cloning of antibiotic resistance gene in E. coli.
there are three basic steps in genetically modifying an organism —
(i) identification of DNA with desirable genes;
(ii) introduction of the identified DNA into the host;
(iii) maintenance of introduced DNA in the host and transfer of the DNA
to its progeny.
11.2 TOOLS OF RECOMBINANT DNA TECHNOLOGY
11.2.1 Restriction Enzymes
In the year 1963, the two enzymes responsible for restricting the growth
of bacteriophage in Escherichia coli were isolated. One of these added methyl groups to DNA, while the other cut DNA. The later was called
restriction endonuclease.
The first restriction endonuclease–Hind II, whose functioning depended on a specific DNA nucleotide sequence was isolated and characterised five years later. It was found that Hind II always cut DNA molecules at a particular point by recognising a specific sequence of six base pairs. This specific base sequence is known as them recognition sequence for Hind II. Besides Hind II, today we know more than 900 restriction enzymes that have been isolated from over 230 strains of bacteria each of which recognise different recognition sequences. The convention for naming these enzymes is the first letter of the name comes from the genus and the second two letters come from the species of the prokaryotic cell from which they were isolated, e.g., EcoRI comes from Escherichia coli RY 13. In EcoRI, the letter ‘R’ is derived from the name of strain. Roman numbers following the names indicate the order in which the enzymes were isolated from that strain of bacteria. Restriction enzymes belong to a larger class of enzymes called nucleases. These are of two kinds; exonucleases and endonucleases. Exonucleases remove nucleotides from the ends of the DNA whereas, endonucleases make cuts at specific positions within the DNA.
Each restriction endonuclease functions by ‘inspecting’ the length of
a DNA sequence. Once it finds its specific recognition sequence, it
will bind to the DNA and cut each of the two strands of the double
helix at specific points in their sugar-phosphate backbones. Each restriction endonuclease recognises a specificm palindromic nucleotide sequences in the DNA. These are groups of letters that form the same words when read both forward and backward, e.g., “MALAYALAM”. As against a word-palindrome where the same word is read in both directions, the palindrome in DNA is a sequence of base pairs that reads same on the two strands when orientation of unless one cuts the vector and
the source DNA with the same restriction enzyme, the recombinant vector
molecule cannot be created. Separation and isolation of DNA fragments : The cutting of DNA by restriction endonucleases results in the fragments of DNA. These fragments can be separated by a technique known as gel electrophoresis. Since DNA fragments are negatively charged molecules they can be separated by forcing them to move towards the anode under an electric field through a medium/matrix. Nowadays the most commonly used matrix is agarose which is a natural polymer extracted from sea weeds. The DNA fragments separate (resolve) according to their size through sieving effect provided by the agarose gel. Hence, the smaller the fragment size, the farther it moves. Look at the Figure 11.3 and guess at which end of the gel the sample was loaded. The separated DNA fragments can be
visualised only after staining the DNA with a compound known as ethidium
bromide followed by exposure to UV radiation (you cannot see pure DNA
fragments in the visible light and without staining). You can see bright
orange coloured bands of DNA in a ethidium bromide stained gel
exposed to UV light.The separated bands of DNA are cut out from the agarose gel and extracted from the gel piece. This step is known as elution. The DNA fragments purified in this way are used in constructing recombinant DNA by joining them with cloning vectors.
11.2.2 Cloning Vectors
plasmids and bacteriophages have the ability to replicate
within bacterial cells independent of the control of chromosomal DNA. Bacteriophages because of their high number per cell, have very high
copy numbers of their genome within the bacterial cells. Some plasmids
may have only one or two copies per cell whereas others may have
198 15-100 copies per cell. Their numbers can go even higher. If we are able
to link an alien piece of DNA with bacteriophage or plasmid DNA, we can
multiply its numbers equal to the copy number of the plasmid or bacteriophage. Vectors used at present, are engineered in such a way
that they help easy linking of foreign DNA and selection of recombinants
from non-recombinants. The following are the features that are required to facilitate cloning into a vector.
(i) Origin of replication (ori) : This is a sequence from where replication starts and any piece of DNA when linked to this sequence can be made to replicate within the host cells. This sequence is also responsible for controlling the copy number of the linked DNA. So, if one wants to recover many copies of the target DNA it should be cloned in a vector whose origin support high copy number.
(ii) Selectable marker : In addition to ‘ori’, the vector requires a selectable marker, which helps in identifying and eliminating nontransformants and selectively permitting the growth of the transformants. Transformation is a procedure through which a piece of DNA is introduced in a host bacterium (you will study the process in subsequent section). Normally, the genes encoding resistance to antibiotics such as ampicillin, chloramphenicol,
tetracycline or kanamycin, etc., are considered useful selectable markers for E. coli. The normal E. coli cells do not carry resistance against any of these antibiotics.
(iii) Cloning sites: In order to link the alien DNA, the vector needs to have
very few, preferably single, recognition sites for the commonly used restriction enzymes. Presence of more than one recognition sites within
the vector will generate several fragments, which will complicate the
gene cloning (Figure 11.4). The ligation of alien DNA is carried out at
a restriction site present in one of the two antibiotic resistance genes.
For example, you can ligate a foreign DNA at the BamH I site of tetracycline
resistance gene in the vector pBR322. The recombinant plasmids will lose
tetracycline resistance due to insertion of foreign DNA but can still be selected out from non-recombinant ones by plating the transformants on
tetracycline containing medium. . The transformants growing on ampicillin containing medium are then transferred on a medium containing tetracycline. The recombinants will grow in ampicillin containing medium but not on that containing tetracycline. But, non- recombinants will grow on the medium containing both the antibiotics. In this case, one antibiotic resistance gene helps in selecting the transformants, whereas the other antibiotic resistance gene gets ‘inactivated due to insertion’ of alien DNA, and helps in selection of recombinants. Selection of recombinants due to inactivation of antibiotics is a cumbersome procedure because it requires simultaneous plating on two plates having different antibiotics. Therefore, alternative selectable markers have been developed which differentiate recombinants from non-recombinants on the basis of their ability
to produce colour in the presence of a chromogenic substrate. In
this, a recombinant DNA is inserted within the coding sequence of
an enzyme, β-galactosidase. This results into inactivation of the
gene for synthesis of this enzyme, which is referred to as insertional inactivation. The presence of a chromogenic substrate gives blue
coloured colonies if the plasmid in the bacteria does not have an
insert. Presence of insert results into insertional inactivation of the
β-galactosidase gene and the colonies do not produce any colour,
these are identified as recombinant colonies.
(iv) Vectors for cloning genes in plants and animals : the lesson of transferring genes into plants and animals from bacteria and viruses which have known this for ages – how to deliver genes to transform eukaryotic cells and force them to do what the bacteria or viruses want. For example,
Agrobacterium tumifaciens, a pathogen of several dicot plants is able
to deliver a piece of DNA known as ‘T-DNA’ to transform normal
plant cells into a tumor and direct these tumor cells to produce the
chemicals required by the pathogen. Similarly, retroviruses in animals
have the ability to transform normal cells into cancerous cells. A
better understanding of the art of delivering genes by pathogens in
their eukaryotic hosts has generated knowledge to transform these
tools of pathogens into useful vectors for delivering genes of interest
to humans. The tumor inducing (Ti) plasmid of Agrobacterium tumifaciens has now been modified into a cloning vector which is no more pathogenic to the plants but is still able to use the mechanisms to deliver genes of our interest into a variety of plants. Similarly, retroviruses have also been disarmed and are now used to deliver desirable genes into animal cells. So, once a gene or a DNA fragment has been ligated into a suitable vector it is transferred into a bacterial, plant or animal host (where it multiplies).
11.2.3 Competent Host (For Transformation withRecombinant DNA)
Since DNA is a hydrophilic molecule, it cannot pass through cell membranes. In order to force bacteria to take up the plasmid, the
bacterial cells must first be made ‘competent’ to take up DNA. This is
done by treating them with a specific concentration of a divalent cation,
such as calcium, which increases the efficiency with which DNA enters the bacterium through pores in its cell wall. Recombinant DNA can then be forced into such cells by incubating the cells with recombinant DNA
on ice, followed by placing them briefly at 420C (heat shock), and then
putting them back on ice. This enables the bacteria to take up the recombinant DNA.
This is not the only way to introduce alien DNA into host cells. In a
method known as micro-injection, recombinant DNA is directly injected
into the nucleus of an animal cell. In another method, suitable for plants,
cells are bombarded with high velocity micro-particles of gold or tungsten
coated with DNA in a method known as biolistics or gene gun. And the
last method uses ‘disarmed pathogen’ vectors, which when allowed to
infect the cell, transfer the recombinant DNA into the host.
Now that we have learnt about the tools for constructing recombinant
DNA, let us discuss the processes facilitating recombinant DNA technology.
11.3 PROCESSES OF RECOMBINANT DNA TECHNOLOGY
Recombinant DNA technology involves several steps in specific
sequence such as isolation of DNA, fragmentation of DNA by
restriction endonucleases, isolation of a desired DNA fragment ligation of the DNA fragment into a vector, transferring the recombinant DNA into the host, culturing the host cells in a medium at large scale and extraction of the desired product.
11.3.1 Isolation of the Genetic Material (DNA)
Recall that nucleic acid is the genetic material of all organisms without exception. In majority of organisms this is deoxyribonucleic acid or DNA. In order to cut the DNA with restriction enzymes, it needs to be in pure form, free from other macro-molecules. Since the DNA is enclosed within the
membranes, we have to break the cell open to release DNA along with other macromolecules such as RNA, proteins, polysaccharides and also lipids. This can be achieved by treating the bacterial cells/plant or animal tissue with enzymes such as lysozyme (bacteria), cellulase (plant cells), chitinase (fungus). The RNA can be removed by treatment with ribonuclease whereas proteins can be removed by treatment with protease. Other molecules can be removed by appropriate treatments and purified DNA ultimately precipitates out after the addition of chilled ethanol. This can be seen as collection of fine threads in the suspension.
11.3.2 Cutting of DNA at Specific Locations
Restriction enzyme digestions are performed by incubating purified DNA molecules with the restriction enzyme, at the optimal conditions for that
specific enzyme. Agarose gel electrophoresis is employed to check the progression of a restriction enzyme digestion. DNA is a negatively charged molecule, hence it moves towards the positive electrode (anode). The process is repeated with the vector DNA also. The joining of DNA involves several processes. After having cut the source DNA as well as the vector DNA with a specific restriction enzyme, the cut out ‘gene of interest’ from the source DNA and the cut vector with space are mixed and ligase is added. This results in the preparation of recombinant DNA.
11.3.3 Amplification of Gene of Interest using PCR
PCR stands for Polymerase Chain Reaction. In this reaction, multiple
copies of the gene (or DNA) of interest is synthesised in vitro using two sets of primers (small chemically synthesised oligonucleotides that are complementary to the regions of DNA) and the enzyme DNA polymerase.
The enzyme extends the primers using the nucleotides provided in the reaction and the genomic DNA as template. If the process of replication
of DNA is repeated many times, the segment of DNA can be amplified
to approximately billion times, i.e., 1 billion copies are made. Such repeated amplification is achieved by the use of a thermostable DNA polymerase (isolated from a bacterium, Thermus aquaticus), which remain active during the high temperature induced denaturation of double stranded DNA. The amplified fragment if desired can now be used to ligate with a vector for further cloning.
11.3.4 Insertion of Recombinant DNA into the Host Cell/Organism
There are several methods of introducing the ligated DNA into recipient cells. Recipient cells after making them ‘competent’ to receive, take up DNA present in its surrounding. So, if a recombinant DNA bearing gene
for resistance to an antibiotic (e.g., ampicillin) is transferred into E. coli
cells, the host cells become transformed into ampicillin-resistant cells. If
we spread the transformed cells on agar plates containing ampicillin, only transformants will grow, untransformed recipient cells will die. Since, due
to ampicillin resistance gene, one is able to select a transformed cell in the
presence of ampicillin. The ampicillin resistance gene in this case is called
a selectable marker.
11.3.5 Obtaining the Foreign Gene Product
When you insert a piece of alien DNA into a cloning vector and transfer it
into a bacterial, plant or animal cell, the alien DNA gets multiplied. In almost all recombinant technologies, the ultimate aim is to produce a desirable protein. Hence, there is a need for the recombinant DNA to be expressed. The foreign gene gets expressed under appropriate conditions.
The expression of foreign genes in host cells involve understanding many technical details. After having cloned the gene of interest and having optimised the conditions to induce the expression of the target protein, one has to consider producing it on a large scale. Can you think of any reason
why there is a need for large-scale production? If any protein encoding
gene is expressed in a heterologous host, it is called a recombinant protein. The cells harbouring cloned genes of interest may be grown
on a small scale in the laboratory. The cultures may be used for extracting the desired protein and then purifying it by using different separation techniques.
The cells can also be multiplied in a continuous culture system wherein
the used medium is drained out from one side while fresh medium is added from the other to maintain the cells in their physiologically most active log/exponential phase. This type of culturing method produces a
larger biomass leading to higher yields of desired protein.
Small volume cultures cannot yield appreciable quantities of products.
To produce in large quantities, the development of bioreactors, where
large volumes (100-1000 litres) of culture can be processed, was required.
Thus, bioreactors can be thought of as vessels in which raw materials are biologically converted into specific products, individual enzymes, etc.,
using microbial plant, animal or human cells. A bioreactor provides the
optimal conditions for achieving the desired product by providing
optimum growth conditions (temperature, pH, substrate, salts, vitamins,
oxygen).
The most commonly used bioreactors are of stirring type, which are
shown in A stirred-tank reactor is usually cylindrical or with a curved base to facilitate the mixing of the reactor contents. The stirrer facilitates even
mixing and oxygen availability throughout the bioreactor. Alternatively
air can be bubbled through the reactor. If you look at the figure closely
you will see that the bioreactor has an agitator system, an oxygen delivery
system and a foam control system, a temperature control system, pH
204 control system and sampling ports so that small volumes of the culture
can be withdrawn periodically.
11.3.6 Downstream Processing
After completion of the biosynthetic stage, the product has to be subjected
through a series of processes before it is ready for marketing as a finished product. The processes include separation and purification, which are
collectively referred to as downstream processing. The product has to be
formulated with suitable preservatives. Such formulation has to undergo
thorough clinical trials as in case of drugs. Strict quality control testing
for each product is also required. The downstream processing and quality
control testing vary from product to product.
