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BioBits
Volume VII Issue III
September 2015
Quarterly E -Newsletter from Bioinformatics Centre (Dic)
Kerala Agricultural University, Thrissur
About Us
The Bioinformatics Centre (DIC) at KAU
runs under the Biotechnology Information
System Network (BTISnet) programme of
DBT, Ministry of Science & Technology,
and Government of India. The Centre was
upgraded to Distributed Information Centre
during 2004 to promote Bioinformatics
research and education. The Centre
enhances access to global information in
life sciences especially plant sciences and
plant biotechnology involving scientists
and students of the University and other
S&T institutions and acts as a support
centre to the Centre for Plant
Biotechnology & Molecular Biology. The
Centre is involved in a wide range of
research work on plant responses to biotic
and abiotic stresses, plant metabolomics
using systems biology approaches, plantpathogen interaction studies and study of
active compounds in anti cancer medicinal
plants. In addition to this, the Centre offers
a credit course in Bioinformatics to post
graduate Plant Biotechnology students
conducts routine training programmes in
Bioinformatics and maintains various
databases relevant to agriculture.
Cover Story
Bioinformatics is not only the hub of all life sciences but also the
cutting edge knowledge for those who would like to make a
breakthrough… Bioinformatics and computational biology involve
the
use
Plant Bioinformatics
techniques
informatics,
statistics,
biochemistry
to
solve
including
computer
biological
applied
science,
problems
mathematics,
chemistry
usually
and
on
sequence alignment, gene finding, genome assembly, protein
structure alignment, protein structure prediction, prediction of
gene expression and protein-ligand interactions etc.
Complex computational and biological problems are now
being addressed and this has led to significant advances in
our understanding of biology. No biological discipline will be
by
these
technological
breakthroughs.
Bioinformatics can revolutionize not only the research sector
but its judicious application can do wonders in transferring
Proteomics & Genomics
News Archive
Discovery Today
Cutting Edge
Our Focus
Letters and Ideas
the
molecular level. Major research efforts in the field include
unaffected
Cover Story
of
knowledge to millions of marginal farmers of the country. This
issue of ‘Biobits’ present before you the recent, most relevant
developments/Research outcomes in Plant Biotechnology/
Bioinformatics.
Plant Bioinformatics
Contents
How opium poppies synthesize morphine?
Many people who live in developing countries do not have access to the pain relief that comes from
morphine or other analgesics. That's because opiates are primarily derived from the opium poppy
plant (Papaver somniferum) and are dependent on the plant health and supply around the world.
After years of leading research on the opium poppy, scientists at the University of Calgary, Canada
have characterized a novel gene that encodes the gateway enzyme in the formation of morphine -
which describes how poppies synthesize the pain killing enzymes. The discovery opens the door to
alternative production systems, aside from the plant itself.
The gene they isolated actually consists of a natural fusion
between two ancestral genes, which encodes the gateway
enzyme in the formation of morphine. It's really interesting to
see these fused genes in a metabolic pathway as it provides
with a new tool to search for something missing in other
plants as well. The findings were published in Nature
Chemical Biology (2015), and detail the missing step to
morphine biosynthesis.
The gateway to morphine biosynthesis in opium poppy is the
stereochemical inversion of (S)-reticuline since the enzyme
Opium poppy plants where the
biosynthesis of morphine occurs.
enzyme yielding the first committed intermediate salutaridine is specific for (R)-reticuline.
A fusion between a cytochrome P450 (CYP) and an aldo-keto reductase (AKR) catalyzes the S-to-R
epimerization of reticuline via 1, 2-dehydroreticuline. The reticuline epimerase (REPI) fusion was
detected in opium poppy.
The researchers said that the isolation of this gene, among many other things, is a key step
toward the reassembly of the pathway to morphine in microorganisms such as yeast. These
efforts could lead to the development of alternative production systems for painkillers such as
morphine, codeine and oxycodone.
Source: http://www.sciencedaily.com/releases/2015/07/150713143657.htm
Proteomics & Genomics
Contents
Oskar protein's structure revealed
The structure of two parts of the Oskar protein, known to be essential for the development of
reproductive cells, solved by scientists of EMBL Heidelberg was recently published in Cell Reports
(2015). The research was carried out with fruit flies, but has implications for other animals, as
many organisms, including humans, also have part of the Oskar protein.
The Oskar protein which has a genetic role is essential
for development process. Embryos that develop from
fruit fly eggs lacking the normal amount of Oskar
protein are unable to form germ cells - cells that allow
reproduction - and so the resulting flies are sterile.
Complete lack of the Oskar protein also prevents the
embryo's abdomen from forming normally which limits
its growth leading to death.
In a healthy egg, Oskar initiates the formation of what's
known as the germ plasm - a gathering of proteins
Illustration of Oskar and its interactions with RNA
and the Vasa helicase.
and RNAs within the cytoplasm, which then goes on
to form a new germ cell. Germ plasm normally forms in a particular position within the egg, but if
Oskar is artificially moved elsewhere, the germ plasm will form in the new location.
The co-author of the work has stated that solving the structure has enabled them to see how the
different parts of the protein function at a molecular level, which could help us to understand
more about this stage of development in a wide range of organisms. Using X-ray crystallography,
the team was able to determine for the first time the structure of Oskar's two domains, called OSK
and LOTUS. The OSK domain is found in some insects, including the fruit fly and the mosquito.
The LOTUS domain is more widespread, being found in bacteria, plants and animals, including
mice and in humans.
They also found that only the OSK domain binds to RNA, specifically three RNAs derived from
genes known to be important to germline development. The LOTUS domain did not bind to RNA;
instead, the team found that LOTUS binds to Vasa helicase, an RNA binding protein with an RNA
dependent helicase which is also one of the essential initial ingredients of the germ plasm. Vas,
like LOTUS, is widely found in other organisms, including animals. The authors have said that
there is still much to learn about how the Oskar protein functions and this work has opened up
lots of exciting new avenues for investigation.
Source: http://www.sciencedaily.com/releases/2015/07/150716135227.htm
News Archive
Contents
Gene 'switch' reverses cancer in common childhood leukemia
Melbourne researchers have shown that a type of leukemia can be successfully 'reversed' by
coaxing the cancer cells back into normal development. Researchers from the Walter and Eliza
Hall Institute showed that switching off a gene called Pax5 could cause cancer in a model of BALL, while restoring its function could 'cure' the disease. The discovery was made using a model of
B-progenitor acute lymphoblastic leukemia (B-ALL), the most common cancer affecting children
and the study was published in the journal Genes & Development (2015).
The researchers stated that along with other genetic
changes, deactivating Pax5 drives normal blood cells to
turn into leukemia cells and they showed for the first
time that reactivating Pax5 enabled the cells to resume
their normal development and lose their cancer-like
qualities, effectively curing the leukemia. One of the
researchers said Pax5 was a gene frequently 'lost' in
childhood
B-ALL.
Pax5
is
essential
for
normal
development of a type of white blood cells called B cells.
From left to right, a red blood cell, a platelet and
a white blood cell are shown.
When Pax5 function is compromised, developing B cells can get trapped in an immature state and
become cancerous. They have shown that restoring Pax5 function, even in cells that have already
become cancerous, removes this 'block', and enables the cells to develop into normal white blood
cells. The research shed light on the function of Pax5, which was one of about 100 genes known to
'suppress' human tumours. When these tumour suppressor genes were inactivated by changes to
the DNA, cancers start to develop.
Forcing B-ALL cells to resume their normal development could provide a new strategy for treating
leukemia. By understanding how specific genetic changes drive B-ALL, it may be possible to develop
more specific treatments that act faster with fewer side-effects.
However genes that are lost in tumour cells are not traditionally drug targets as it is very difficult to
develop drugs that restore the function of genes lost during cancer development. However by
understanding the mechanisms by which Pax5 loss causes leukemia can begin to look at ways of
developing drugs that could have the same effect as restoring Pax5 function. The genetic switch
technology used to study Pax5 could also be used to understand 'tumour suppressor' genes in other
cancers as well.
Source: http://www.sciencedaily.com/releases/2014/06/140617094035.htm
Contents
Discovery Today
Chloroplast tubes play a key role in plants' immune defense
Researchers at University of California, Davis and the University of Delaware, Newark have found
that chloroplasts better known for taking care of photosynthesis in plant cells, play an unexpected
role in responding to infections in defense mechanism.
Inter-organellar communication is vital for successful innate immune responses that confer defense
against pathogens. However, little is known about how chloroplasts, which are a major production
site of pro-defense molecules, communicate and coordinate with other organelles during defense.
When plant cells are infected with pathogens, networks of tiny tubes called stromules extend from
the chloroplasts and make contact with the cell's nucleus, the team discovered. The tubes are likely
to deliver signals from the chloroplast to the nucleus that induce programmed cell death of infected
cells and prepare other cells to resist infection. The work has been published online in the journal
Developmental Cell (2015).
Chloroplasts send out dynamic tubular extensions called
stromules during innate immunity or exogenous application of
the pro-defense signals, hydrogen peroxide (H2O2) and salicylic
acid. Interestingly, numerous stromules surround nuclei during
defense response, and these connections correlate with an
accumulation of chloroplast-localized NRIP1 defense protein
and H2O2 in the nucleus. These results support a model in
which stromules aid in the transport of pro-defense signals into
Infection causes tubes called stromules
(blue) to grow from chloroplasts (purple) to
the nucleus of a plant cell (yellow) carrying
signals that boost immune defenses.
the nucleus and other subcellular compartments during
immunity.
This opens a new area of understanding how the chloroplast communicates with the nucleus, and
likely with other organelles within the cell. Chloroplasts in neighboring uninfected cells also
produce stromules, apparently signaling the nucleus to switch on genes that make cells more
resistant to infection. Stromules were first described more than 50 years ago, and their role in a
specific biological process has been solved now.
Source: http://www.sciencedaily.com/releases/2015/06/150625145244.htm
Cutting Edge
Contents
Researchers have engineered the world’s first artificial ribosome
Researchers in the US have developed a synthetic molecular structure called the Ribo-T and it can
be placed inside a living cell to produce specialized proteins and enzymes at almost the same
efficiency as an actual ribosome.
Ribosomes are dense, complex structures inside all living cells, that catalyze a constant stream of
protein chains by linking amino acids together in the order specified by messenger RNA (mRNA)
molecules. These cellular workhorses are basically in charge of decoding DNA, and now scientists
have manufactured a molecular device that can not only produce protein chains in a test-tube
almost as well as a real ribosome, but can also churn out enough protein in bacterial cells without
any natural ribosomes to keep them alive.
The team from the University of Illinois at Chicago and
Northwestern University, says not only will the Ribo-T help to
better understand how our own ribosomes function, but it
could lead to more effective drugs and next-gen biomaterials,
with these little protein factors churning out whatever the need.
Natural ribosomes float around inside a cell in two halves (or
subunits), and only link up when they need to link some
protein chains together. To keep the lab-made ribosome from
linking up with the naturally occurring ones - which would kill
World’s first engineered
artificial ribosome
the cell - the scientists tethered the two halves together. Because Ribo-T is tethered shut and can
never separate like a natural ribosome, all kinds of new and amazing things can be cooked up
inside, such as unique polymers that can help us track processes inside the ribosome. By
creating an engineered ribosome where the ribosomal RNA is shared between the two subunits
and linked by these small tethers, the scientists could actually create a dual translation system.
While the engineered ribosomes exceeded all expectations in terms of how effective they are, they
are far from perfect. Reporting in Nature, the team says that while bacterial cells with no natural
ribosomes at all could live off the proteins produced by an army of Ribo-Ts, they grew at half the
speed of normal cells.
One of the scientists told that the tethered ribosome is good, but not as good as 'normal'
ribosome". The team is hopeful that with a few years under its belt, Ribo-T be a whole lot more
efficient than it is now. It’ll never catch up to the several billion years of evolution that our
ribosomes have had to perfect their craft.
Source: http://www.sciencealert.com/researchers-have-engineered-the-world-s-firstartificial-ribosome
Our Focus
Contents
The Centre is involved in a wide range of research work like plant-pathogen interaction studies,
study of active compounds in medicinal plants, in-silico analysis of phytochemicals against various
diseases and creation of databases and their maintenance. In silico docking studies on phyto
compounds are carried out to predict the preferred orientation of one molecule to a second
when bound to each other to form a stable complex. The binding efficiency, interaction and dock
score would help a long way in identifying novel phytocompounds against serious diseases.
Contents
Letters & Ideas
This particular column is especially for readers and those who are interested in the field of
Bioinformatics. Here we are creating a new opportunity to share your valuable ideas with senior
scientists. So post your comments and suggestions to mail [email protected] or [email protected].
The Team
Dr. P.A.Nazeem (Coordinator)
Priyanka James, Radhika R.,
Ravisankar V., Bincy Baby,
Vipin A.M., Sangeetha P. Davis
& Cicy Joseph.
How to Reach Us
Bioinformatics Centre (DIC),
ITBT Complex, Kerala Agricultural University, KAU P.O,
Thrissur, Kerala-680656.
Website: www.kaubic.in
Email: [email protected], [email protected] or [email protected]
Ph: 0487-2371994, Fax: 91487-2371994.