Mutagenesis and its Testing Methods Review Article *O.S. Vivekanandan

Transcription

Mutagenesis and its Testing Methods Review Article *O.S. Vivekanandan
Review Article
THE SCITECH JOURNAL ISSN 2347-7318 ISSN 2348-2311 Online
SAMANTHI
Mutagenesis and its Testing Methods
*O.S. Vivekanandan
Dept. of Biotechnology/ Bioinformatics, Vels University, Pallavaram, Chennai – 600 117, India
Abstract
Mutations are changes in the genetic makeup that can either be small or large, can result in a changed phenotypic expression that can be
neutral, beneficial or harmful to the organism. Mutations can be spontaneous or deliberately induced the later having several applications
including for industrial biotechnology. Understanding mutagenesis is important for obtaining an insight into the complex gene
behavior/function mechanisms. Mutation detection and quantification is enhanced to a great extent by the technological advancements in the
cytogenetic and molecular techniques. In this review, the types of mutations and the historical perspectives of mutation analysis are discussed.
Also, the various types of mutations, numbering twenty five, including the somatic, germinal and morphological mutations are described.
Mutation screening and analysis methods vary in accordance to the nature of mutations and the type of sample material. Here, fourteen
different mutagenesis screening methods which can be applied for a variety of samples including plant, animal and malignant tissues are
reviewed and discussed.
Key words: Mutations, history of mutation research, mutagenesis, mutation types, mutation detection.
Introduction
Mutations are the genetic alterations either induced or spontaneous
in genetic material. Evolutionary advance has been evinced in the
study from the identification of the phenomenon itself,
technological innovations for its detection both in vivo and in vitro,
in selected test systems and general populations. The study of
induced mutations had its beginning more than 75 years ago, with
the work of Herman Muller (1928), who developed a method for the
recognition of mutations that are induced by X-ray in Drosophila.
Chemical mutagenesis has received a major thrust during the past
decade following 1) the observation of a close association between
mutagenecity and carcinogenecity, 2) the amount of exposure of
human system to the multitude of chemicals in every day. In recent
year's studies in mutation, research entered a new era due to
advances made in the screening techniques. This has lead to a
significant advancement in the study of chemical mutagenesis. This
has warranted undertaking a survey of available literature on
mutagenesis.
nature, rather than having been small and continuous, may well have
been large and discontinuous. de Vries (1900) called these large
effects. The mutation theory proposed by de Vries (1900) has
formed an alternative to the Theory of Natural Selection put forward
by Darwin. de Vries was working with the evening primrose
(Oenothera lamarkiana) in which new and strikingly different types
of plants occasionally appeared breeding true to the new type. On
the basis of this work, that new species would originate as a result of
large discontinuous variations or mutations rather than from the
gradual accumulation of numerous small hereditary differences in
size, shape, color, etc., by natural selection. However, his theory
turned to be based on a variety of changes in the genome of
Oenothera, including tetraploidy, trisomics, reciprocal
translocations and balanced lethal systems. However, these
hereditary changes did not represent genetic mutations even though
they breed true and remain distinct from parental type. These
spurious recombinant mutants in Oenothera are the results of a
unique situation not to be found in all species and therefore they
cannot serve as a general mechanism for evolution.
The mutation research dates back to 1791 when Setch Wright
noticed a Norwegian lamb with unequal short legs in his flock of
normal legged sheep. Wright thought that it would be worthwhile
having a whole flock of short-legged sheep, which could not get
over the low stone fence and damage the crop in the adjacent fields.
In the successive generations, this trait was transferred and a breed
was developed where all sheep had short legs. This character
resulted from a change in the hereditary material that occurred in a
particular cell. This will be carried in all cells descending from the
parent cells. The point mutation was discovered at a time when the
science of genetics did not even have its birth. The short legged
sheep are known as Ancon breed.
Mutation is an unequal phenomenon of interest in the history of
science. Throughout the 20th century, mutations have been at the
heart of science of heredity. The place of mutants in the history of
genetics has been underestimated due to the induction of mutations
often entitled a mode of enquiry that included altering the
environment partly by means of new tools like radium, X-ray and
chemicals. The effect of mutations may be great, or may be so small
that refined statistical or genetic methods are needed to detect the
difference between mutant types. The field of mutagenesis started in
the year 1953, when the structure of DNA was known. The early use
of nitrous acid and hydroxylamine as mutagens in eukaryotes,
Historical Perspective
Received: September 2014
Accepted: September 2014
*Corresponding Author
Email:[email protected]
In the late 19th century, prior to the discovery of Mendal's work, de
Vries and others had put forth a theory, that hereditary changes in
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initiated induced mutagenesis. This lead to the development of
methods for the metabolic activation of mutagens by microsomal
preparations and the selection of a mutant tester set for the
qualitative characterization of the mutagenic activity of chemicals.
Today, DNA sequencing has replaced the use of diagnostic
mutagens, but studies of this kind formed the foundation of
molecular mutation research
Genesis of Mutation Research
The term mutation is derived from a Latin word 'Mutare' (to
change), which was used earlier to describe the changes in
hereditary material. During early 1900, investigators in
Netherlands (de Vries, 1901) and rediscovered the works of George
Mendal. The growth of new science formed the framework for the
eventual inquiry into the nature of gene. These scientific
innovations prompted to know how the external factors induce
changes in the natural genetic order. Most of the early work in this
new line of research took place in Europe. Charles Darwin, in his
early work on the “Origin of Species by Natural Selection” (1859)
used the term 'mutation' to describe the production of variation in
organisms. The term mutation was then used widely in the scientific
literature. It was difficult to determine when the term mutation was
first used in relation to the field of genetics and modern biology. This
new word was used by Hugo de Vries during 1886, to denote the
appearance of variation in the plant evening primrose (Oenothera
lamarkiana) (de Vries 1900 a, 1900 b). Latter, he used this term as
the key title word in his volume “The Mutation Theories” in which
he gave an elaborate description on the production of morphological
changes observed in Oenothera (de Vries, 1901). During 1901, de
Vries has proposed, that knowledge on principles of mutation will
certainly, in future enable the production of artificial mutation in
plants, that is, the creation of better varieties of plants and animals.
Auerbach (1976) used the term mutation to describe the changes in
quality, quantity and arrangement of genes.
During the early years of 1905, the idea of using chemicals to induce
mutations began to intrigue investigators. Franz Wolff (1909) and
Elizabeth Schiemann (1912), who independently conducted
mutation experiments with bacteria and Fungi (Bacillus prodigious
and Aspergillus niger) using various oxidizing agents. Many
interesting discoveries were being made in the field of genetics in
the first three decades of twentieth century. These findings had
stimulated, thinking about the artificial induction of mutations.
Muller (1928) has showed unequivocally that radiation is a
mutagen. He has also developed the concept of 'mutation rate'. This
has prompted many researchers to initiate the studies to determine
the mutagenecity of chemical compounds. It was finally established
that chemicals could induce heritable mutations. Auerbach and
Robson (1946) established that chemical warfare agent mustard gas
was mutagenic on Drosophila sp.
Late in the 1940's, the relationship between mutagenesis and
carcinogenesis also began to intrigue some investigators. There is a
danger of producing mutations in somatic cells by radiation, which
may result in cancers, leukemia etc., in mitotically dividing tissue.
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The New Dimensions
The genetic toxicology begins its new chapter during 1950's.
Barthelmess (1956) had been interested in the mutagenecity of
chemicals and had collaborated many publications on this subject.
The results of research in genetics within the last two decades call
for increased consideration of possible cytogenetic side effects and
their consequences in organisms exposed to toxicants. Joshuva
(1962) began his studies on the hazardous chemicals to the germ
cells of man. During 1950's there was an issue of whether routine
toxicity testing should include assays for mutagenecity before
approval of the common chemicals that are put to human use.
Auerbach (1960) stated that more and more chemicals are used in
therapeutics, food processing and other industries; the testing of
substances for mutagenic ability will become a necessary protective
measures. During 1960's a concern was developed to detect the
hazards of chemicals on human health, not only for the present
generation but also for those yet unborn.
Although it is clearly desirable that mutation research should be
carried out on a wide range of organisms as possible, extrapolation
to man can be made with the most confidence where they are derived
from work with a mammal. The mouse is the mammal offering the
most advantages for genetical studies, in addition, a great many
mutants are known and the linkage map is fairly well worked out.
The most productive method has been derived on mouse system is
the specific-locus method that help in assessing the genetic hazards
of chemical and physical agents (mutagens). The technique also
helps to elucidate the nature of mutation process.
The environmental mutagenic society (EMS) had its origin during
1968 headed by Hollaender at USA. The objectives outlined are the
encouragement of interest in potential hazard of mutagens in human
environment, publication on methodologies of mutagenecity
testing, publication of newsletter and formation of register of
chemicals tested for mutagenecity in particular system. Thus,
officially born EMS has prompted the initiation of staring such
societies in other countries. In India, the Environmental Mutagenic
Society on India (EMSI) was first started by Dr.Sundram at BARC,
Mumbai. This society got affiliation with the EMS of USA. The
dedication and hard work of the scientists has provided an excellent
list of hazardous chemicals which can induce mutagenesis in human
population.
Kinds of Mutation - a glimpse
Mutation occurs more frequently in large group of genes, which are
converted into large chromosomes than in smaller groups, therefore,
mutations could occur at random. The mutation process only a
mechanical loss or dimination of the gene by deletion of
chromosomal material or an increase of the gene may lead to reverse
mutations. The gene is an 'ultra microscopic particle'. A large cell
contain thousands of genes, a change in a single invisible one of
these molecules can profoundly affect the physical and chemical
properties and result in new gene composition. The gene molecules
are also found to some extent in mitochondria and chloroplast
(Muller, 1947). Mutations may either spontaneous or induced;
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accordingly they are termed as spontaneous mutations and induced
mutations respectively. The change in genome involving
chromosome parts, whole chromosome or whole chromosome sets
are called chromosomal mutations or chromosomal aberrations.
The chromosomal mutations are proved to be of great significance
in applied biology, agricultural, animal husbandry and medicine.
The point mutations refer to alterations of single base pairs of DNA
to a small number of adjacent base pairs. The point mutations are
classified as intragenic suppressor mutations, extragenic suppressor
mutations, missence suppressor mutations, frame shift mutations
and physical suppressor mutations (Anthony et al., 2000).
Spontaneous Mutation
Mutations enhance spontaneous induction of chromosome breaks
and somatic chromosome mutations. Spontaneous mutation occurs
during cell division. Mutagenic damage produced by alkylating
agents may get converted to mutant DNA sequences. These
chemicals also induce sex linked lethal and somatic reversions in
Drosophila.
Ahuja and Dhayal (2007) reported that petal spotted spontaneous
mutants of four species were identified from the populations of
Gossypium hirsutum having three different genotypes. These
mutants were found to have some desirable morphological and fiber
technological characters. This might be possible as a result of
mutation of pigmentation but also other traits. Transgenic cell lines
are also useful to analyse the relation between gene mutations and
chromosome aberrations. Spontaneous mutations are frequent in
meiotic cells, through a process of recombination and are caused by
inherent instability in gene expressions. Forward mutations are
change away and reverse mutations are change to the wild type
allele. These mutations lead to the loss of function of a gene or to
new function. The forward mutation is the single nucleotide pair
substitution at DNA level or at protein level.
I. At DNA Level
1. Transition
Atransition is the replacement of a base by another base of the same
chemical category. For e.g. purine replaced by purine, pyrimidine is
replaced by pyrimidine.
2. Transversion
A transversion is the opposite category of the transition, where a
base of chemical category is replaced by another base of different
chemical category. For e.g. purine is replaced by pyrimidine,
pyrimidine replaced by purine.
3. Addition or Deletion Mutation
This is a type of mutation where a single base pair addition, deletion
or substitution leads to degeneration of the code and existence of
translational or termination codons.
II. At protein Level
4. Silent substitution Mutation
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The mutation changes are coded for an amino acid into another
codon for the same amino acid. The alteration of AAA to AAG is not
detected and both code for the same amino acid lycine. These
alterations are the silent mutation.
5. Non-Sense Mutation
These types of mutations have a considerable effect on the function
of proteins. The codon from one amino acid is replaced by
translation or termination of a codon. It was identified that the HOX
AB nonsense mutations in a family with hand – foot genetical
syndrome. The stop codon truncates and eliminates or reduces the
ability of the protein to bind DNA .
6. Null Mutation
This type of mutations are otherwise called nothing mutations. That
is in or close to active site of a protein leading to lack of function.
This completely abolishes the activity of the gene.
7. Missense Mutation or Synonymous Mutation
The codon for one amino acid is replaced by a codon for another
amino acid resulting with a substitution of a chemically similar
amino acid. This type of mutation has a less severe effect on the
function and structure of proteins.
8. Frame shift Mutation
Non-sense mutations lead to the premature termination of
translation. They have considerable effect on protein function. The
lesions are called frame shift mutations. Acridine derivatives, the
mutagens induce mutation by suppressing CNG base sequence and
results frame shift mutations at these regions. The frame site
mutations influenced by T4 DNA polymerase. This plays a variety
of role in the metabolic events leading to frame shift mutations by
transitions and transversions. The target into for these mutations is
the G-C base pairs. Bhatia et al., (2007), detected that a single base
change in the putative promoter region of one of the clinical isolates
of Mycobacterium tuberculosis that behaves like a gain - of function mutations. Frame shift mutations cause drastic
consequences for the protein by adding or removing one or several
base sequences. This results with a shift in the frame of DNA base
pairs. The carcinogenesis is proven frame shift mutagen.
9. Point Mutation / Gene Mutation
Point mutation refers to alteration of single base pairs of DNA or to
small number adjacent base pairs. Point mutations are classified into
intragenic suppressor mutations, missense suppressor mutations,
frame shift suppressor mutations and physiological suppressor
mutations. Induction of point mutation in somatic cells in culture
can be as quantitative as in microbial systems because a large
number of cells are easily obtainable. The data on somatic mutation
in mammalian cell cultures both spontaneous and induced will be of
particular value when they are compared with the data on mutation
frequencies at the same or different loci in vitro somatic mutations
itself may play an important role in development, oncology, immune
mechanisms and aging. Point mutations affecting the Uid R
regulatory gene were sought to investigate the regulation of Uid A.
the binding of the regulatory molecule may facilitate the binding of
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the other one in a cooperative process. The Uid R - d mutations do
not modify Uxu AB operon expression in a wild type strain contrary
to the behavior of Ux UR – d mutations (Curlas Blanco et al, 1986).
Gene mutation result in the synthesis of defective enzymes, which
have lost their catalyst properties totally or partially. If the enzyme
loses its activity, the biochemical reaction leading to the formation
of a product may be absent. The product may be a metabolic, needed
for growth and hence has to be added from outside. This addition
may activate the mutational effect (Sulochana Das, 1981). The 'S'
gene region of hepatitis B virus is responsible for the expression of
surface antigens and includes the determinant region. The kinds of
point mutations were identified within 'S' region. High rate
mutations were found in chronic hepatitis patients and their family
members (Mehnet Ozaslam et al, 2007). The cause for portal
hypertension in Indian populations is due to G 20210 prothrombin
gene mutation (Sanjay Sharma et al, 2006). The point mutation in
DNA binding domain of mex R gene could be one of the factors
contributing to the possible drug resistance in patients having
Cornell keratitis (Suman et al, 2006).
Mutations in genes trigger cell death and premature ageing disorder.
This may also lead to the lung disorders in youngsters. The modified
purines, a- amino purines and b- N-hydroxy amino purines are
known to cause point mutations in prokaryotes. The vibration in
space vehicles is also responsible for inducing point mutations. It
causes G-C to A-Tmutations.
10. Somatic Mutations
Somatic mutations are not passed on to progeny. Mutations in
somatic cells have an impact on the well-being and survival of
individuals. Somatic mutations in genes would help to regulate the
cell cycle may lead to cancer mutations occur in a special type of
genes called proto-oncogenes, resulting from one progenitor cell is
called a clone. This is linked with mutagenesis. The external and
internal factors mutate the spindle formation induce gene or spindle
formation repressor gene. This leads to abnormal proliferation of
somatic cells resulting in cancer.
11. Germinal Mutations
Germinal mutations occur in germ cells, play an active role in the
determination of sex. These mutants are expressed only in the male
descendants. The sudden appearance of a novel phenotype in a
pedigree where there is no such previous records of such novel
appearance is determined through germinal mutations.
12. Morphological Mutations
Morphological mutations will affect the outwardly visible
properties like color, shape and size of an organism.
13. Lethal Mutations
New lethal mutations are recognized by their effects on the survival
of organisms.
a) Dominant Mutations
A dominant mutations offer the great advantage of appearing in the
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generation immediately after mutational event, in contrast to
recessive, which may be delayed for many generations.
b) Dominant lethal Mutations
A dominant lethal mutation (DL) is the one, which kills an
individual heterozygous for it, carrying it in a single dose. The
dominant will have arisen in egg or sperm prior to fertilization and
could kill the zygote during development. The primary genetic
lesion responsible for dominant lethal mutation is chromosome
breakage. The assay can be used to study the problems of interacting
both synergetic and antagonistic between known mutagens. In
Drsophila melanogaster, ethylmethane sulfonate induced X- linked
temperature sensitive lethal and semi-lethal mutants. The
temperature sensitive at 15 loci affect the fidelity of mitotic
chromosomal behavior in Drosophila (David Smith et al, 1985). The
dominant lethal egg may die and disappear without a trace. The
uterine tumor kills the placental cell after mitosis or after the
implantation of the fertilized egg. There is a potentiality for not
developing the process of differentiation that is necessary to
produce a fetus. The late fetal death results in subnormal size, and
posses restricted development in structures.
14. Conditional Mutations
Based on the environmental conditions mutations may be a)
restrictive-occurs in certain environment b) permissive-occurs in
different environment.
15. Biochemical Mutations
Biochemical mutations are identified by the loss or change of some
biochemical function of the cells. This will lead to the development
and expression of inborn errors of metabolism. Many such losses in
function of mutation are found to be recessive and some are
dominant.
16. Gain-of -function mutations
During these mutations, a kind of new phenotype is produced due to
a dominant allele. Mutant genes are used as the probes to
disassemble the constituent part of a biological function and to
examine their working and interactions (Anthony et al, 2007).
17. Insertional Mutations
This method relies on the fact of the exogenous DNA inserted
randomly into the genome, can produce mutations if inserted
fragment interrupts a gene or its regulatory sequences (Alberts et al,
2002).
18. Chromosomal Mutations
The changes in genome involving chromosomal parts, whole
chromosomes or chromosome sets are called chromosomal
aberration or chromosomal mutations; this is of great significance in
applied science. The history of chromosomal mutations can be
traced back to 1947, when Auerbach and Robson induced
mutational changes in Drosophila by using nitrogen mustered. In
India, Swaminathan (1950) used the chemical agent in the
improvement of crop plants.
19. X - linked Recessive Mutations
If a new mutation occurs in a 'X' chromosome, the chances are 2:1
that it occurs in a female, since she has two 'X' chromosomes. If the
mutation occurs in males and the trait is very rare so that the
possibility of his wife being a carrier can be regulated, the mutant
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phenotype has virtually no chance of being exposed until the grand
children generations. Ashadevi et al, (2005) studied two-eye color
and two using mutants in Drosophila species. The x- linked
mutations were identified on the typical criss-cross patterns of
inheritance of the phenotypes.
20. Autosomal Recession Mutation
A recessive autosomal mutant will be expressed only if it is
transmitted in gametes from both parents
21. De novo Mutations
A new mutation that was not inherited from either parent is called de
novo mutation. These mutations, where the effects are not
influencing the fitness of an individual, can accumulate due to
genetic drift. Mutation is the mechanism upon which natural
selection acts, providing the advantages, new traits or
disadvantageous traits that die out with weaker organisms.
Homeotic mutants are useful in understanding morphogenesis –
development and the interplay of environment and genotype. In one
example of such mutants, the mosquito proboscis labella are
modified. These mosquitoes are not able to pierce skin and obtain
blood from the mammalian host (Thomas et al, 1971).
22. Para-mutation
Para-mutation is an interaction between alleles that lead to direct the
heritable change, at the locus with higher frequency and sometimes
invariability within the time span of a generation. The first instance
of para-mutation leading to the irregular allelic interaction as
observed in rabbit ear region, in Pissum sativum and also at 'R' locus
in maize (Alexander Brink, 1973).
23. Mitochondrial Mutations
Human ageing depend on the decline of respiratory function
heading to the increased production of reaction oxygen species
(ROS) and free radicals on mitochondria due to enhanced electron
lack of the respiratory chain recently it has been shown that
mitochondrion due to enhanced electron lack of the respiratory
chain. Recently it has been shown that mitochondrial mutations are
also influencing human ageing. The oxidative modification and
mutation of mitochondrial DNA (mtDNA) were found to increase
exponentially with age in human and animal tissue. Mitochondrial
mutations can lead to various syndromes such as CPEO (Chronic
progressive external ophthalmoplesia), KSS (Kears-Sayre
Syndrome), MERRF (Myoclonic Epilepsy with ragged red fibers),
MELAS (Mitochondrial encepahalomyopathy, lactic Acidosis and
stroke – like episodes), NARP (Neuropathy, Ataxia and Retinitis
Pigmentosa), MNGIE (Myoneurogastro intestinal disorder and
encephalopathy), recurrent myoglobinuria due to coenzyme Q 10
deficiency etc., and affecting major organs. Parkinson's and
Alzheimer's diseases can also be caused by mtDNA mutations.
Recent reports showed that somatic and homoplastic mutations in
mtDNA causing multiple neonatal deaths. The mt DNA mutation
disease might be caused only when the bearer is exposed to an
environmental toxin like amino glycoside induced ototoxicity.
The Leigh syndrome is due to the basal ganglionic lesions caused by
variations in mitochondrial and nuclear gene. A novel homoplasmic
T11984 C missense mutation occurs in ND4 gene, which replaces a
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highly conserved amino acid tyrosine with histidine. This mutation
alters the secondary structures of ND4 sub unit. Mutation at the
DFNBI locus which encode connexin 26 (CX 26) and connexin 30
(CX30), proteins respectively, are main cause for sporadic and
familial non-syndromic hearing impairment in many populations.
Specific mtDNA mutations have been found to be associated with
non-syndromic hearing impairment. Deletion and three point
mutations in mtDNA are found to be the cause for these mutations.
Oxidative stress is a condition established due to an imbalance
between antioxidant levels and reactive oxygen species in variety of
diseases like diabetes, cancer, ageing, Alzhmeir, anthrosclerosis,
rheumatoid arthritis, multiple sclerosis, muscular dystrophy, cancer,
etc., Recently male sterility is also attributed to this condition, might
be due to the damage of mitochondrial and DNA (mutation) in the
spermatozoa. The excess reaction oxygen species (ROS) and low
antioxidant levels in the semen might cause mitochondrial DNA
mutations and vice versa in oligoasthenozoospermia men. This
result in impairing the fertilizing capacity of spermatozoa (Kunal et
al, 2009) Mitochondrial DNA is known for high mutation rates
caused by lack of protective histones, inefficient DNA repair
systems and continuous exposure to mutagenic effects and oxygen
radicals. It was suggested that the extent of mitochondrial DNA
mutations might be useful in the prognosis of cancer
outcome/and/or the response to certain therapies. The presence of
mutations correlated with Human Papilloma virus infection in the
patients suffering from cervical carcinoma. Mutations in either
mtDNA or nuclear gene encoding oxidative phosphorylation may
lead to clinical disorders like mitochondrial encephalomyopathies
in pediatric patients. The study will be useful in genetic diagnosis
and counseling of mitochondrial disease in men in India. A novel
nonsense mutation (CH994T) in the mitochondrial ND 4 gene,
which replaces threonine with isoleucine, was observed in all of the
oligoastheno zoospermic men but not in any of the normo
zoospermic fertile men (Deepa selvi et al, 2006).
24. Cataract Mutation
The specific locus mutations, dominant cataract mutations, protein
change mutations and enzyme activity mutation are affected by
certain physical and chemical factors.
25. Coat Color Mutation in Animals
Pioneering studies in this field were carried out at the return of the
century by William Castle and two of his students. A series of
manuscripts of 1917 and 1918 had showed that the coat color
genetics was a useful way “to assist embryology and biochemistry in
filling the links between germ cell and adult in specific cases”.
Many coat color mutations are available, however a rudimentary
knowledge of pigment chemistry and biochemistry provided a basis
with which to interpret genetic interaction experiments. For
example, it was remarked that there was a reciprocal and genetic
relationship between black and yellow coat color in rabbits was due
to the different alleles acting at the same locus. This has lead to the
conclusion after 50 years of observation that the biochemical
process responsible for determining whether hairs were black or
yellow acted on a single substrate produced by the product of the
albino rats.
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During 1920's, systematic attempts were initiated at several
research institutions to catalog and preserve different mutations and
in addition to develop inbred, strains of animals so that the effects of
different mutations could be studied on a constant genetic
background. Most of the knowledge on coat color gene action has
come from mice and other mammals have confirmed the principles
behind coat color mutations. Many coat color mutations in mice and
virtually all those in other mammals are of spontaneous origin. A
special class of mutations at a small number of loci has been
induced, experiments were designed to measure and characterize
genotoxic effects of radiations and chemicals. In many research
laboratories, experiments were designed to detect loss of function
mutations at one of several different loci. In most mammals other
than mice, a small number of loci have been recognized as coat color
mutations. A temperature sensitive loss of function mutation in
tyrosinase produces a distinctive phenotype known as the
“Himalayan Mutations” in rabbits, mice or guinea pigs and also
responsible for the characteristic appearance of Siamese coats. Coat
color mutations are usually classified based on cellular/ and / or
developmental processes that are disrupted, pigment cell
differentiation/ migration/survival, biochemical synthesis of
melanin intracellular trafficking membrane sorting of pigment
granules or pigment type-switching. In mammals, melanin is a
complex polymer, derived from oxidized derivatives of tyrosine,
and is deposited with in sub cellular organelles called
'melanosomes'. Melanin synthesis requires a series of enzymes for
different oxidation steps. A complete loss-of function for tyrosine
leads to mutational effect.
In mice, mutation in a large class of coat color genes produces a
generalized pigment dilution, platelet storage pool deficiency and
abnormal lysosomal trafficking. Mutations in several genes can
alter pigment type-switching, including the agouti gene itself and
melanocortin receptor gene, which encodes the receptor for agouti
protein expressed on malanocytes. Most interesting group of coat
color mutations are those that cause regular patterns of stripes or
spots as in Zebras, Tigers, Leopards, or Giraffes. It is presumed that
this is likely to be pheomelanin or eumelanin alternating with
number of pigments. In human albinism refers to a generalized
dilution or loss of pigmentation and is broadly grouped into
conditions that affect eyes, skin and hair, approximately ten
different genes were identified to mutate and cause albinism. Coat
color variations are due to melanism pigment synthesis in house
mice in Asia is described and found to be darker in humid habitats
than those in drier habitats. The coat color variations might be due to
the selective forces like bacterial degradations and
thermoregulation (Lai et al, 2007). Evidence was provided that the
expression of the aberrant coat color results from the action of an
autosomal recessive mutation in Cheetahs (Acinonyx jubatus) (Van
Aande and Arun Van Dyk, 1985).
A. Structural changes in Chromosomes
I. Changes in number of genes
Deletion/ Deficiency
A chemical agent induce two breaks in a chromosome may produce
interstitial deletions (loss of segments). An intragenic deletion may
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occur within a gene or mutagenic deletion will occur due to the
breaks in two or several thousand genes. These deletions are
responsible for tumor formation or lethal mutations (Anthony et al,
2000).
Duplication
A structural change in the chromosome produced due to the addition
of an extra copy of some chromosome region. Duplications supply
additional genetic material capable of evolving new functions.
II. Changes in Gene Arrangement
Insertion
Two breaks occur in a chromosome, and rotate at 180° before
rejoining with the two and fragments. Inversions do not change the
overall amount of the genetic material, and in the phenotype.
Inversion may be peracentric or pericentric.
Translocations
Two non-homologous chromosomes mutate by exchanging parts,
the resulting rearrangements are called translocations. A segment
from one chromosome is exchanged with a segment from another
non-homologous chromosome. This kind of mutation is of great
importance in agriculture since it helps to control insect pests.
Reciprocal translocations are also seen in cancer cells
Two schools of thought have come to explore the origin of
chromosome rearrangements 1. Russian geneticist considered that
rearrangements were “illegitimate cross - over” and were formed
when two different chromosomes or regions of the same
chromosome happened to lie in juxtaposition during the process of
mutation. 2. The second school headed by Stadler, assumed that
breakage always preceded rearrangement formation at any two
broken ends. The target theory has remained a guiding principle in
mutation research. The deletions are due to the removal of a piece of
chromosome, which require two breaks. The origin of these
deletions is still a puzzle. The oxygen modifies the types of deletions
and modifies the target molecule and that act as a protective agent.
Chromosomes number
The aneuploids may be monosomics (2n-1), nullisomic, trisomics,
double trisomics and tetrasomics. The trisomics are responsible for
inducing human genetic disorder.
1. Loss or gain of a part of the chromosome set is called aneuploidy.
2. Loss or gain of a whole chromosome set is called euploidy.
3. Addition of one or more sets of chromosomes is called polyploidy.
Polyploidy may be autopolyploids / allopolyploids
Methods - Mutagenesis Screening
The polyploidisation of colchicines in plants has provided an
impetus for developing new avenues for research in mutagenesis.
The initiation of investigations on this line of research on
mutagenesis was systematically standardized and attempts were
made to explore the properties of different mutagenic chemical
agents. This was first made by Levan (1949) and his collaborators by
applying a technique called Allium test. For animal materials, the
mutagens are applied either through feeding or injecting or post –
treatment cultures. The capacity of inducing chromosome breakage
is a property of several chemical agents. Some of the mutagenic
chemicals affect sulph-hydryl groups of proteins and others act
through their influence on hydrogen bonds of nucleic acids.
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Physical and chemical structure of chromosomes Researches in the
19th and 20th centuries established that chromosomes bear the
hereditary materials or 'genes' in a linear sequence of the permanent
fibrous constitution. The chromosomes are the components of an
eukaryotic and prokaryotic nucleus that are formed at the time of
cell division. The chromomere hypothesis assumed that
chromosome is composed of longitunally aligned chromatin
granules joined by an achromatic thread. The chromonema
hypothesis visualized a uniformly thick continuous structure in a
chromosome, capable of spiralisation. Recent analysis showed that
chromosomes are the continuous deoxy - nucleoprotein fiber in
which condensed and decondensed segments may alternate. Most of
the evidences, on ultra structure analysis of chromosomes indicate
the presence of fibrils of 2-3 nm in diameter. Heterochromatic and
euchromatic segments are characterized by different staining cycles
in the different phases of growth and division. The centromere,
secondary constriction regions, telomeric segments and other
heterochromatic regions must fit in the molecular structure of the
genophore, since they are the regions, which were differentiated
functionally. The occurrence of divalent cations, histones and even
lipids are often regarded as transverse incorporation. Chromosomes
are the dynamic structure that has a major role in differentiation,
development and control the reproduction of species. The
precipitates of the pus cells were found to contain carbon, nitrogen,
hydrogen, oxygen and phosphorous which are now known as DNA .
The basic structural unit of chromatin called the 'nucleosome' was
described by Roger Korenberg (1974). The nucleosomes are
structurally complex in their organization. The DNA is wrapped
around histones in nucleosome core particles and sealed by histone
H1. Histone proteins lined to the linker DNA between nucleosome
core particles. Nucleosome core particles contain 146 base pairs of
DNA wrapped around histone core. Thus, the packaging of DNA
with histones yields a chromatin fiber of a chromosome. The
chromatin fibers are folded to form a compact structure in a
chromosome. Adenine, thymine and guanine, cytosine rich DNA is
wrapped around histones in nucleosome core particles and sealed by
histones H1. Non-histone proteins are lined to the linker DNA
between nucleosome core particles. Each chromosome will have a
specialized unstained region called centromere or kinetochore.
Recently, it was the showed that centric region also contain some
amount of DNA. The chromosomes are formed during divisional
phase of the cell cycle of a nucleus. Chromosome damage has been
observed to be a reliable index of the measure of genetic damage to
human. The Discovery of the fluorescent banding pattern in
chromosomes has proved to be an effective tool in the identification
through high-speed scanning devices. The chromosome does not
follow a normal pattern of behavior in malignant cells. Vigorous
research on the induction of chromosomal breakage, polyploidy and
mutation by physical and chemical agents is being carried out in
different parts of the world. Varied techniques are developed in the
recent years to understand the different aspects of chromosomes and
their role in mutations. The principles, applicability and drawbacks
of these techniques are discussed by Sharma and Sharma (1980).
Chromosomal aberrations are quantitatively, a significant class of
mutational event for physical and chemical mutagenesis. It forms an
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index for the study of mutational damage. The techniques employed
in the study are short-term tissue culture, experiments on somatic
cells and experiments on animals. The in vivo and in vitro
productions of mutational changes are complex, since, the
administration and absorption of the mutagenic chemical in the
target cells. The compound may get detoxified in vivo by tissues.
Before quantitative data derived in mutagenesis testing, the
laboratory animals are used to make meaningful statements
concerning man. However, more information is needed to 'bridge'
these two species. It has been concluded that man is more sensitive
as compared to the mouse for the production of interchanges by
mutagens. Most of the chemicals tested are very specific in their
time and mode of action (Kihlman, 1966) Pre – fixatives and
fixatives.
The cells are pre-treated with some specific chemicals for cleaning
the cytoplasm, separating the middle lamella of a cell and bringing
scattering of chromosomes through spindle inhibition during cell
cycle and also to remove cell deposits. Acid and enzyme
preparations are applied for cleaning cytoplasm and cell separation
through digestion. Recently, Swaminathen and Natarajan (1957)
have demonstrated that vegetable oils like sesamum oil brings
scattering of chromosomes in metaphase. The pre-fixed cells are to
be fixed in desired fixatives to kill the tissue without causing any
distortion for the components. Some of the chemical fixatives are
either lethal or decompose the cell components. Hence, the freezing
method of fixatives was developed to minimize distortion of the
tissue, least diffusion and no significant effect on the enzyme
systems. In general, the fixatives are classified into non-metallic and
metallic. After suitable fixation, the tissue is processed for further
study. Different schedules are followed for serial sections and smear
preparations. The microtomy is followed in order to show
arrangement of cells in a tissue and sequence of stages in the
divisional cycle. The procedure entails the operations like washing,
dehydration, clearing, infiltration, embedding, microtome cutting,
removal of sections and mounting on synthetic and natural resins.
I. Plant Material
1. Mitotic Studies in Root Tip Cells
A. Squash or Smear preparations
The sectioning method has been largely replaced by smear or squash
techniques. These methods are found to be of great advantage to
bring about rapid and crucial observations. In smear, the cells are
directly spread over a slide prior to fixation without any
pretreatment to secure cell separation. Pollen mother cells in plants
are the most convenient objects for smears. In squash, on the other
hand, special treatments are needed for proper separation of
individual cells. Then the cells are stained and squashed on a slide.
b. Staining
The structure and behavior of chromosomes can be studied only
after they are stained by using 'vital' or 'non-vital' stains. The tissue
retains the color due to chemical configuration called autochrome of
the dye. The dyes are generally termed basic or acidic based on their
chemical nature and behavior. In cytological studies, several types
of mordents are used for proper stain adherence to the tissue.
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c. Different Types of Staining Procedure
The Feulgen reaction is the most effective with regard to
chromosome staining. The chemistry of the staining has been
worked out by different authors. There is a specific test for
localizing DNAin situ. Carmine is another widely used dye for
chromosome staining. Orcein dye was first employed as a
chromosome stain by Lacour in 1941. The other stains such as
chlorazol black, crystal violet, Haemotoxylin, Brazillin, Lacrmoid,
Toluidine blue in different laboratories for specific study of the
tissues. After staining the tissue, whether in the form of section or
smear, is mounted on a suitable medium for observation. The
mounting media such as balsam, euparal, lacto phenol, cedar wood
oil, glycerin jelly etc., are used.
2. Mitotic Studies in Leaf Tips
Sharma and Mookerjee (1955) gave a schedule for preparing leaf tip
squash. The leaf tips are pre-treated with saturated aqueous solution
of aesculine and is fixed in acetic ethanol mixture (1:1), stained in
aceticorcein and squashed.
3. Pollen Grains
The anthers were dissected from a young flower bud. They are
smeared on a drop of acetic-carmine solution on a clean dry slide.
Pollen mother cells are smeared for the study of meiotic
chromosomes. The mitotic division in endosperm tissue can also be
developed by acetic orcein squash method (Sharma and Varma,
1960).
II. Animal Material
The usual sources of materials are larval tails, ganglia and
spermetogonial cells. These materials are sectioned through
paraffin block preparations. The bone marrow cells of mammals
were developed to study mitotic divisions in higher group of
animals. Temporary squash / smear preparation were made from the
testis of a male grasshopper for the study of meiotic chromosomes.
Certain special technique, for the study of the differential nature of
chromosome segments, was followed to study the special
chromosomes, centromere, secondary constriction,
heterochromatin, salivary gland chromosomes, lamp-brush
chromosomes, polytene chromosomes, prochromosomes, pollen
grains, embryo sac mother cells, endosperm and the study of
nucleolus. The mitotic behavior of chromosomes in lower group of
plants like algae and fungi were also studied through special
techniques. Human leukocyte cultures were made to analyze the
mutational behavior of chromosomes in man. Anomalies in the
chromosome structure and variation in number can be studied
through karyotype analysis. Buccal smears can also be made to
study the mutational behavior of sex chromatin (Bar bodies).
Chemical mutagens can be effectively administered to habrobracon
aducts by aerosols, feeding, topical application and microinjection.
Habrobracon eggs can be immersed in aqueous solution, which
contain possible chemical mutagens. Mutational events like
dominant lethal mutations, recessive lethal mutations and
translocation can be measured in sperms, differing cell types during
oogenesis of eggs. The habrobracon test is uniquely rapid and
reliable for assaying dominant lethality. Studies with animal cells in
tissue culture have shown that, as a rule, there appears to be a good
SAMANTHI
correlation between the chromosome breaking activities of
chemicals in plant and animal cells. Although a chemical, which
produce aberration in plant root tips usually, also does it in animal
cells, the types of effect may vary in different two materials. For
example, 5-bromo deoxy uridine, a thymidine analog induces
chromosomal mutations in tissue culture of Chinese Hamster Ovary
(CHO) cells, but does not cause any visible damage in the
chromosomes of bean root tips (Hollaender, 1972).
III. Mutation Analysis from Malignant Tissue
The conspicuous features of cancer cells are the high frequency of
mitotic divisions, chromosomal aberrations and numerical
variations of chromosomes. The rapid advance in research on
cancerous materials has been responsible for the development of
several techniques for culturing malignant cells in vitro. The
chromosome studies of these materials form the source of
knowledge of the mutational changes in malignant tissues.
IV. Chromosomal Banding Technique in Mutational Studies
Human chromosome segments are analyzed through differential
banding patterns of chromosomes. The technique has brought a
revolution in the study of karyotype that permits precise
identification of individual chromosome segments. This technique
visualizes the molecular sequence of DNA and its mutational
changes.
V. Sister chromatid Exchanges (SCE)
The SCE techniques demonstrate DNA segregation and give a
uninemic interpretation of DNA organization within chromosomes.
The technique permits the identification of the chromatids of each
chromosome or the basis of differential staining intensities. These
exchanges are either spontaneous or accelerated artificially. This
method has been used in detecting in vivo exchanges in mammalian
systems as a test environmental mutagens for studying chromosome
structure, identifying active and inactive sex chromosomes and also
DNA replication patterns in higher group of organisms exposed to a
variety of mutagens.
VI. Flowcytometry
Flowcytometry provides a rapid sensitive and quantitative
measurement of various testicular germ cell types. The information
could provide an analysis on the ploidy nature of germ cells as
induced by mutagens. Flowcytometry combines many advantages
for rapid phenotypic and genotypic analysis of individual cells.
Since, the DNA content of germ cell changes distinctly during the
various steps of proliferation and transformation in
spermatogenesis, DNA flow cytometry offers a method to monitor
with relative ease such changes in dispersed testicular cells (Toppari
et al, 1988).
VII. Teratology
The mutagenecity of chemical compound may also be assessed by
teratogenecity assay in animal system. The foetotoxic effect of a
mutagen may be evaluated through the induction of exposed
pregnant animals (Wilson, 1965, and Gupta et al. 1978). The fetuses
cleared and stained with Alizarin red - S stain.
VIII. Micronucleus Test
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Micronucleus test was developed in order to detect the structural
chromosomal abnormalities in bone marrow cells of animal in vivo.
The assay was introduced by Schimid (1975 & 1982). Micronuclei
originate from chromatin, which lag during anaphase, indicating
spindle disturbance. It is suitable for routine screening of mutagens
and it may identify effects not covered by bacterial assays. This test
is also able to identify inhibition of proliferation in the bone marrow
by strong mutagens.
IX. Sperm Head Abnormalities
Mutations are influenced either by a physical or chemical agent in
male germinal cells of men and animals. These agents induce
damage in DNA and results with many abnormalities in the
production of gametes namely the spermatozoids. The technique
involves a series of steps and separating the cauda epididymis which
is smeared to get spermatozoids. The techniques appear to give
slightly more reproducible results than when an acute single dose is
given; usually larger dose may be given over 5 days.
X. Comet Assay
The technique was first described by Singh et al (1988), gained
popularity as a standard technique for evaluating the DNA damage/
repair. It involves the encapsulation of cells in a low-melting-point
agarose suspension, lysis of cells in neutral or alkaline (pH > 13)
conditions, and electrophoresis of the suspended lysed cells. This is
followed by visual analysis with staining of DNA and calculating
fluorescence to determine the extent of DNA damage.
The comet assay and micro gel electrophoresis (MGE) were first
introduced by Ostling and Johanson (1984). This is a neutral assay
in which the lysis and electrophoresis were done under neutral
conditions. Staining was done with acridine orange. The image
obtained looked like a “comet” with a distinct head, comprising of
intact DNA and a tail, consisting of damaged or broken pieces of
DNA, hence the name comet assay was given. The assay can be
performed on a variety of samples, which can be obtained as a single
cell population e.g. Peripheral blood lymphocytes, nasal and buccal
epithelium from clinically or occupationally exposed human
population and for in vitro studies on cell lines e.g. CHO V 79,
mouse lymphoma or cultured human lymphocytes and bone marrow
cells. Both DNA and repair studies can be conducted.
XI. Molecular assay in mutation detection
The standard electrophoretic procedures could be combined with
other methods, as they are developed and automated. It is possible to
screen as many as ten different proteins. Once a variant type was
found, the parents could be studied to see if it was inherited or was a
new mutation.
XII. Polymerase Chain Reaction (PCR)
PCR based in vitro mutagenesis is an important tool that allows
defined mutations to be made in vitro to cloned DNA. Prior to its
conception, approaches focused on the generation of random
mutation, such as those induced by radiation or chemicals.
However, these methods did not allow mutations in a specific gene
or chromosomal location to be investigated. PCR based in vitro
mutagenesis, which is now commonly used in many laboratories
SAMANTHI
can provide critical information on the regulation of gene
expression as well as protein structural function.
1) Numerous strategies were developed to target defined region of
DNA, including
a. Base (s) substitution
b. Deletion or insertion
c. Chimeric gene generation
d. Multiple site mutagenesis
2) The mega primer method and the quick change method, however,
none of these approaches can be applied to all diverse mutagenesis;
the methods using digestion with type Igs restriction enzymes and in
vitro ligation, to generate mutations. This technique is applicable to
diverse mutagenic purposes in molecular biology studies. A target
gene is amplified in two separate PCR fragments by four PCR
primers. This method is rapid and highly efficient and has been
applied successfully to several different genes. This method is
successful at generating mutations not only single site substitutions
but also for multiple site substitutions, insertions, deletions,
chimeragenesis and random mutagenesis. This method is also used
for detecting the presence and diversity of low level mutations in
human tumors with their potential prognostic value and their
putative influence on the ability of tumors to resist during treatment
and or metastasize (Hughes and Moody, 2007).
XIII. The Host Mediated Assay
The host-mediated assay is a simple technique that attempts to
bridge the gap between in vitro microbial studies and definitive tests
in mammals. This is a practical procedure for evaluating potential
mutagenic agents in mammals. This is also, a valuable tool for
characterizing mutagenic agents. The assay was developed to
determine the ability of laboratory animals to either potentate or
detoxify compounds concerning their mutagenecity. In addition to
the studies in mammals, it is essential to conduct the in vitro assay.
XIV. Mammalian cell culture
There are four different methods for mutation selection in
mammalian cell cultures.
A. Mass selection method
The method involves the expressing mass culture and extrinsic
agents or specifically altered growth media.
B. Lethal – Growth method
Involves differential growth of mutants and non mutants cell and
selection killing of growing non-mutant cells.
C. Thymine less 'Death' method
By the ' thymine less' death method a situation is created in which the
parental cell die and the mutant cells do not grow but are able to stay
alive in the selective environment. Thymidine deprivation does not
lead to unbalanced growth and death in cells in which protein
synthesis is also blocked.
D. Replica plating method
The procedure involves cloning of cells as micro cultures in plates
and replication of the micro cultures with the replicator. A number of
temperature sensitive mutants were isolated by the replica plating
procedure. The capacity of inducing chromosome breakage is a
property of several chemical agents. Some of the mutagenic
chemicals effect sulphydryl groups of protein and others act through
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their influence on hydrogen bonds of nucleic acids
E. Molecular assay in assessing mutagenesis
A variety of methods have been developed for introducing
mutations into cloned genes, all of which involve the use of enzymes
and chemicals that cleave, degrade or synthesize DNA. These
mutations can be generated through either simple lestions or
insertions or substitutions of single base, or systematic deletions,
insertions or substitutions of clusters of bases. A systematic method
can be used to generate a large number of deletions or insertions
with in the general region of interest. These mutations are screened
by fine – resolution restriction mapping and or DNA sequencing.
Small deletions or insertions can be generated systematically either
by partial digestion with pancreatic DNAase I, or by partial
digestion with restriction enzymes. These methods have their own
advantages and disadvantages. Several methods have been
developed to generate sets of deletion mutants that back
progressively more sequences from one and or the other of the target
DNA. Out of these methods, the digestion with exonuclease III is
proved to be an ideal method to analyse the molecular aspects of
mutagenesis. Oligonucleotide mediated mutagenesis is used to add,
delete or substitute nucleotides in a segment of DNA. The method
can be used to alter individual codons in protein coding sequences or
to generate defined changes in protein coding sequences or to
generate defined changes in sequences that have a regulatory
function. Oligonucleotides used to create deletions or insertions or
to substitute two or more contiguous nucleotides.
Restriction enzymes are used to recover the foreign DNA from the
double standard replicating form of the recombinant bacteriophage
genome that has been sequenced. Occasionally difficulties are
encountered in obtaining a particular mutation. The nature of
mutation, target sequence and vector are the encountered
difficulties. X-ray diffraction of protein crystals and chemical
modification of the side chains of the amino acids that form the
primary sequence of protein and the two methods involved in the
direct study, to understand the structure and function of a protein.
The simplest method of localized random mutagenesis is to react a
short fragment of double standard DNA with a chemical mutagen
such as nitrous acid or hydroxylamine and to close the population of
mutagenised fragments into a recombinant plasmid that carries the
remainder of the wild - type gene. Another method in the molecular
analysis of mutagenesis is the treatment of single standard DNA
with chemicals that damage all four bases. Point mutations can be
introduced into double standard DNA by incorporating base
analysis with various types of DNA polymerases (Sambrook et al,
1989).
Conclusion
Understanding mutagenesis is important for unraveling the way
genes function and behave. Mutations are important focus areas to
study gene interactions and the factors affecting gene behavior. The
advancements in technology in the detection methods have helped
in studying mutagenesis and mutation induced changes with clarity.
As mutations can be induced and targeted changes in the genes and
gene sequences can be achieved, this area has tremendous potential
SAMANTHI
for direct beneficial applications
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Citation: O.S. Vivekanandan (2014) Mutagenesis and its Testing Methods The Scitech Journal Vol.1(10) 07-17
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