Yeast as a model organism in genetics, cell and molecular biology

 Budding yeast ( Saccharomyces cerevisiae ) is extensively used as a model

organism for studying cellular processes in evolutionarily distant species,
including humans. Studying the phylogenetic tree of life shows humans and yeast
shared a common ancestor over a billons years ago. So, it is quite remarkable to
know how a unicellular organism is related to human beings.

Some of the attributes which makes yeast as a model organism in genetics, molecular
and cell biology are;

1. Simplest organization:
 Yeast is a simplest eukaryotic organism.
 Cell wall consisting of glucans, mannans and proteins
 Periplasmic space with hydrolytic enzymes
 Plasma membrane consisting of a phospholipid bilayer and many different
proteins
 Nucleus with nucleolus
 Vacuole as storage and hydrolytic organelle
 Secretory pathway with endoplasmic reticulum, Golgi apparatus and
secretory vesicles
 Peroxisomes for oxidative degradation
 Mitochondria for respiration
 Yeast combines many advantages of bacterial with eukaryotic genetics

2. Genomic study model:

 In 1996, Saccharomyces cerevisiae become first eukaryotic organism whose
genome is fully sequenced.
 Genome of cerevisiae is well studied,consists of 12 million bps of DNA and
contains about 6000 genes. Many genes important for human biology were
discovered by studying their homologous in yeast cell.
 Similarly nearly 1000 yeast genes are members of orthologues genes of human
which are associated with human disease. For most of these genes, they are
functional in yeast but not in human, this indicates deletion mutation in these
genes.
 Yeast nuclear genome has 16 chromosomes.
 Yeast genome is approximately three times larger than that of E. coli, although it
is far more manageable than the genomes of more complex eukaryotes, such as
humans.
 The yeast chromosomes contain both centromeres and telomeres sequence.
 Only a small percentage of yeast genes has introns; non coding sequence of RNA
transcript.
3. Contains extra chromosomal DNA:
 Yeast contains extra chromosomal double stranded circular plasmid DNA
 more than one plasmid can be transformed in a yeast cell at a time.

4. Economic:
 Yeast are easy to culture and maintain in laboratory environment

5. Short generation time compared to other higher organisms.

6. Experimental study model:

 Gene manipulation is not complicated.
 Many fundamental aspects of eukaryotic cell such as DNA replication,
transcription, translation, mutation, etc are understand on the basis of yeast
study
 Yeast can be “transformed” with replicating plasmids. Transformation is
efficient, although not as efficient as in E. coli.
 Yeast has an incredibly efficient systems for homologous recombination

7. Yeast consists of both haploid and diploid form:

 S. cerevisiae has two vegetative stages, haploids and diploids
 The haploid yeast genome consists of about 12,500 kbp
 Haploid and diploid form are interchangeable. Mating pairs of haploid cells fused
to give diploid cell, while diploid cell on sporulation gives haploid cell. This makes
genetic study easier. An exogenous DNA can be easily integrated into yeast
genome.

Uses of yeast as model organism:

 To study ageing complexity of human beings:
 Yeast cells divides mitotically but the number of division in finite before
cell dies(30-40 division), called replicative ageing. This is analogous to
ageing profile of human stem cells.
 Yeast cell dies when it stay longer time in post mitotic stationary phase
which is compared to human neuron of central nervous system.
 Human goes ageing because most human somatic cell do not express
sufficient telomerase to prevent telomere attrition. This can be studied in
yeast cell by knocking telomerase.
 To study the cell cycle
 Genetic analysis of mitochondrial biogenesis
 Use to study basic principles of eukaryotic gene expression and regulation such as
lac operon, trp operon etc
 Use to study signal transduction pathway in higher organisms
 Different new technologies in genetics and systemic biology are developed by
studying yeast as a model
  Use to study human genetic diseases

Escherichia Coli
Escherichia coli, or E. coli for short, is a Gram-negative, rod-shaped bacteria that is a
normal inhabitant of the lower gastrointestinal tract of warm-blooded animals.
Scientists estimate that E. coli first evolved between 120 and 160 million years ago,
about the same time as the appearance of mammals. It is likely that E. coli has been
living in the colons of mammals for the entire history of both groups. Further evidence
for this symbiosis is the relatively rare ability of E. coli to utilize lactose, which is the
sugar of milk, found only in mammals. Also, E. coli are able to survive in the presence of
bile salts, which are caustic and used in digestion.
In addition to thriving in the colon, E. coli can also survive outside the body.
Environmental E. coli can be spread through feces as the bacteria pass out of the body.
These two habitats are about as opposite as you can get. The colon is relatively stable,
warm, anaerobic, and nutrient-rich. Outside of the colon, conditions can be extremely
harsh and variable, much colder, aerobic, and provide fewer nutrients.
Model Organism
The fact that E. coil is able to survive such variable conditions is one advantage that
led to its use as a model organism. A model organism is a species that is extensively
studied to understand a specific phenomenon, expecting that the knowledge gained can
be applied to other species as well.
E. coli has many attributes that make it an ideal candidate for use as a model organism.
Let's discuss the five major attributes that make E. coli an excellent model organism.
Attribute 1: E. coli is a single-celled organism. There are no ethical concerns about
growing, manipulating, and killing bacterial cells, unlike multicellular model organisms
like mice or chimps. They are also tiny cells, so in a small laboratory you can have flasks
containing billions of cells that take up very little room, allowing many experiments.
Attribute 2: E. coli is able to reproduce and grow very rapidly, doubling its population
about every 20 minutes. This is helpful in a lab situation where waiting for subsequent
generations to produce experimental data can be the rate-limiting step. With E. coli it
is as easy and fast as letting them grow overnight. Trying to study the same process in
subsequent generations of elephants, for example, would require several generations of
scientists and more elephants than we have on the planet!
Attribute 3: E. coli can survive in variable growth conditions. As we discussed earlier,
this leads to it being very adaptive yet forgiving in lab situations. Culture media
containing simple and inexpensive ingredients and nutrients can successfully spur E. coli
to grow and divide.
Attribute 4: Most naturally occurring strains of E. coli are harmless. Those food-
poisoning E. coli that sprang to mind earlier are the exception, not the rule. When
scientists first started using E. coli for lab experiments, they chose a strain that was
harmless. This means that studying E. coli poses little threat to researchers and the
public.
Genetic Manipulation
Attribute 5: E. coli can be genetically manipulated very easily. The genetics of E. coli
are well-understood and can be readily manipulated, or engineered. This is the most
important and multifaceted attribute contributing to the use of E. coli as a model
organism.
E.Coli and its life cycle
Biology of E.coli • Escherichia coli ( commonly abbreviated E. coli) is a Gram-negative,
facultative anaerobic ,non-sporulating and rod-shaped bacterium that is commonly
found in the lower intestine of warm-blooded organisms . •
Most E. coli strains are harmless, but some can cause serious food poisoning in humans
The harmless strains are part of the normal flora of the gut, and can benefit their
hosts by producing vitamin K2, and by preventing the establishment of pathogenic
bacteria within the intestine. • E. coli and related bacteria constitute about 0.1% of gut
flora, and fecal-oral transmission is the major route through which pathogenic strains
of the bacterium cause disease. • Cells are able to survive outside the body for a
limited amount of time .There is, however, a growing body of research that has
examined environmentally persistent E. coli which can survive for extended periods of
time outside of the host . • The bacterium can also be grown easily and inexpensively in
a laboratory setting, and has been intensively investigated for over 60 years.
3. 3. Biology of E.coli • E. coli is the most widely studied prokaryotic model
organism, and an important species in the fields of biotechnology and microbiology,
where it has served as the host organism for the majority of work with recombinant
DNA. • Cells are typically rod-shaped, and are about 2.0 μm long and 0.5 μm in diameter.
• It can live on a wide variety of substrates. • E. coli uses mixed-acid fermentation in
anaerobic conditions, producing lactate, succinate, ethanol, acetate and carbon dioxide.
• Optimal growth of E. coli occurs at 37°C (98.6°F) but some laboratory strains can
multiply at temperatures of up to 49°C (120.2°F). • Growth can be driven by aerobic or
anaerobic respiration • Strains that possess flagella are motile. • E. coli and related
bacteria possess the ability to transfer DNA via bacterial conjugation, transduction or
transformation, which allows genetic material to spread horizontally through an
existing population
Life cycle of E.coli • E. coli reproduces by two means: cell division, and the transfer of
genetic material through a sex pilus (conjugation). •

Advantages of E.coli as a model organism

Rapid reproduction and small size. •Under optimal conditions, they can reproduce every
20 mts. , in a mere 7 hrs., a single bacterial cell can give rise to more than 2 millions
descendants. •
Thus enormous numbers of cells can be grown quickly , so that even very rare mutations
will appear in a short period of time
Consequently , numerous mutations in E. coli everything from colony appearance to drug
resistance , have been isolated and characterized
E.coli is easy to culture in the laboratory in liquid medium or on solid medium within
petriplates.
Role of E.coli in biotechnology
E. coli plays an important role in modern biological engineering and industrial
microbiology
The work of Stanley Norman Cohen and Herbert Boyer in E. coli, using plasmids and
restriction enzymes to create recombinant DNA, became a foundation of biotechnology
Considered a very versatile host for the production of heterologous proteins,
researchers can introduce genes into the microbes using plasmids, allowing for the mass
production of proteins in industrial fermentation processes
Genetic systems have also been developed which allow the production of recombinant
proteins using E. coli. One of the first useful applications of recombinant DNA
technology was the manipulation of E. coli to produce human insulin. • Modified E. coli
cells have been used in vaccine development, bioremediation, and production of
immobilised enzymes. • E. coli cannot, however, be used to produce some of the larger,
more complex proteins which contain multiple disulfide bonds or proteins that also
require post-translational modification for activity.
9. 9. E.coli Genome • The first complete DNA sequence of an E. coli genome
(laboratory strain K- 12 derivative MG1655) was published in 1997. • Despite having
been the subject of intensive genetic analysis for approximately 40 years, a large
number of these genes were previously unknown. • When the genome was sequenced as
part of Human genome project ,it was found to be a circular DNA molecule 4.6 million
base pairs in length, containing 4288 annotated protein-coding genes (organized into
2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA)
genes. • The coding density was found to be very high, with a mean distance between
genes of only 118 base pairs. • Greater gene density is due to a combination of factors:
(1) bacterial genes have no introns, (2) neighboring genes are very close together
throughout the genome; i.e., there are hardly any big regions of non-coding DNA
between genes.