BIOmics Hands-On Workshop & Conference
Weizmann Institute of Science
Rehovot, Israel
LECTURE ABSTRACTS
|
Levy A |
Genetic and epigenetic mechanisms of gene
expression rewiring in hybrids and polyploids |
|
Chattoo
BB |
Rice transgenics leading
to broad spectrum disease resistance |
|
Margalit
H |
Domain pairs underlying protein interaction
networks |
|
Protein-protein interactions: biophysics and
design |
|
|
Samish I |
Defining the fold space of the membrane proteome
|
|
Lai L |
From structure to
systems based drug design |
|
Wolfson
HJ |
Atomic resolution modeling of large macromolecular
assemblies |
|
Milo R |
Optimality in carbon metabolism |
|
Pilpel
Y |
Optimal translation |
|
Aharoni
A |
Systems biology: integrating metabolomics
and transcriptomics |
|
Protein-protein interaction inhibitors: application
to cystic fibrosis |
|
|
Lancet D |
Molecular recognition and biological evolution |
Avraham Levy1,
Itay Tirosh2, Sharon Reikhav1,2,
Michal Kenan-Eichler1, Cathy Melamed-Bessudo1 and
Naama Barkai2
Genetic and epigenetic mechanisms of gene
expression rewiring in hybrids and polyploids
Departments of 1Plant
Sciences and 2Molecular
Genetics, Weizmann Institute of Science, Rehovot,
Israel
Genome merging, in interspecific
hybrids and allopolyploids, is associated with novel patterns of gene
expression. We have analyzed the
genetic and epigenetic basis for this rewiring in two model systems, namely a
yeast hybrid between Saccharomyces cerevisiae
and S. paradoxus,
and a synthetic wheat hybrid and allopolyploid analogous to bread wheat. In
yeast, in collaboration with Naama BarkaiÕs laboratory, we have analyzed how hybrid-specific
gene expression patterns are generated from the divergence in regulatory
components between the parental species. We have distinguished changes in
regulatory sequences of the gene itself (cis) from
changes in upstream factors (trans). Expression divergence was mostly due to
changes in cis. Changes in trans were
condition-specific and reflected mostly differences in environmental sensing.
In the hybrid, over-dominance in gene expression occurred through novel cis-trans interactions or, more often, through modified
trans regulation associated with environmental sensing. We will discuss the phenotypic impact
of hybrid-specific expression patterns. In wheat we have previously shown rapid genetic and
epigenetic alterations in genes or transposons at the
onset of hybridization and/or in nascent allopolyploids. As small RNAs
are candidates for affecting these events, we have analyzed the changes in
small RNAs (Micro and siRNAs)
populations in hybrids and allopolyploids and their connection with genes and transposon expression. We show that small RNA populations are altered in hybrids
and polyploids with the strongest changes observed
just after polyploidization. Overall, in the first generation of the
polyploid, there was a massive suppression of siRNAs that corresponds to repeats and transposons. This is consistent with the observed
transcriptional activation of transposons upon polyploidization and supports the role of siRNAs in heterochromatinization
and repression of transposons. These works emphasize
how different levels of regulation, namely genetic, epigenetic and
environmental, can bring about hybrid-specific expression patterns in lower and
higher eukaryotes.
Bharat B Chattoo
Rice transgenics leading to broad spectrum
disease resistance
Department of Microbiology and
Biotechnology Centre, M.S.University of Baroda, Vadodara (Gujarat), India
A long term
strategy for ensuring food and nutritional security requires the development of
durable non-race-specific resistance against pathogens. Rice homologue of Arabidopsis Constitutive Disease
Resistance (CDR1), an aspartate protease, which is
one of the essential components for Systemically Acquired Resistance response
(SAR), has been functionally validated. Transgenic Arabidopsis over-expressing OsCDR1 accumulated
high levels of Salicylic Acid (SA) and showed several fold induction of the defence related genes PR1 and PR2, but not PDF1.2.
The
transgenic plants also exhibited oxidative burst, and this was associated with
the establishment of SAR, suggesting a role for OsCDR1 in SA mediated
disease resistance signalling pathways. This was further supported by the
observation that over-expression of OsCDR1 in transgenic Arabidopsis plants enhanced disease resistance
against infection by P. syringae pv. tomato and Peronospora parasitica. Local infiltration of intercellular fluids (IF) from
transgenic Arabidopsis plants into
the leaves of wild type plants induced the systemic defence
response and a mobile elicitor activity was detected in the IFs.
Over-expression OsCDR1 in rice led to
constitutive activation of defence-related genes such
as PBZ1/PR10, PR1 and helped acquire enhanced resistance against phytopathogens.
In a complementary approach, several pathogenicity related genes were identified and
characterized in the
rice blast fungus M. oryzae. Insertional
mutagenesis identified a gene MGA1 which is required for the development of ŌappressoriaÕ. The mutant was unable to cause either foliar
or root infection. In addition, a novel transporter ABC4 was identified to have
role in fungal pathogenesis. We have also developed a comprehensive and
integrated database called Genomic
Resources of Magnaporthe oyzae (GROMO) to facilitate work on the rice blast pathosystem. It contains information on genomic sequences,
mutants available, gene expression analysis, localization
of proteins etc., obtained from a variety of repositories, as primary data. In
addition, prediction of domains, pathways, protein-protein interactions, sumolyation sites and biochemical properties that were
obtained after computational analysis have also been included as derived data. In
the GROMO project, an effort has
been made to integrate information from different databases like BROAD MIT Magnaporthe database, Agrobacterium
tumefaciens-mediated transformation (ATMT) M. oryzae database, Magnaporthe
grisea – Oryza sativa
(MGOS) and Massive Parallel Signature Sequencing (MPSS) databases to generate
novel information, make insightful predictions and to better understand the
Rice-M. oryzae pathosystem.
The database is currently available at: http://gromo.msubiotech.ac.in/
Hanah Margalit
Domain pairs underlying protein interaction networks
Department of Molecular Genetics and Biotechnology,
Faculty of Medicine,
The Hebrew University of Jerusalem, Jerusalem,
Israel
Many proteins are constructed of domains, which are their functional and main structural units. The modular structure of proteins has allowed their classification by the domains comprising them. This classification system was extended recently to protein interaction networks and to the domain pairs that play a role in mediating the interactions. In my talk I will describe several of our studies into this domain-pair-based modular structure of protein-protein interaction networks: 1) domain pairs as evolutionary conserved building blocks of protein interaction networks. 2) Partial order of domain pairs when used as interaction mediators and its application to prediction. 3) Intra-domain features that allow versatility in domain-domain interaction. These analyses emphasize the complex structure of protein interaction networks and hint at their finer levels of granularity, beyond the domain-pair level.
Back to top of pageGideon Schreiber
Protein-protein
interactions: biophysics and design
Department of Biochemistry, Weizmann Institute
of Science, Rehovot, Israel
Proteins are the working horse of the cellular machinery. They are
responsible for diverse functions ranging from molecular motors to signaling.
Maybe the most common dominator of all proteins is their ability to interact
with one another, and with many other types of molecules, whether small or
large. Not only do proteins interact with most known chemical components, they
do so specifically. In other words, they interact at a specific location, with
a specified affinity and kinetics. One of the most exiting fronts in
computational protein-protein interactions is the use of the existing knowledge
on protein-protein interactions for interface design. Design can be aimed in
increasing the affinity of a complex or changing its binding specificity. Here,
I will present what we have learned during the last decade on the architecture
of protein-protein binding sites, and the forces holding them together. Next, I
will show how we utilized the gained knowledge to develop protein design
methods. The first method utilizes the algorithm PARE, developed in my lab to
specifically enhance the rate of association and by this the affinity of the
protein-complex. The success of the method is demonstrated on the protein pairs
TEM-BLIP and Ras-Ral. The second design method
comes to change the binding specificity between a pair of proteins, while
maintaining the high affinity. To be able to do this successfully we took
advantage of the modular architecture of protein-interfaces, and devised a
method to alter specifically one module. This was done by
seeking in the PDB a similar module (in structure) but not in sequence.
This module was incorporated into the interface of TEM1-BLIP replacing the
original one. This resulted in a TEM1-BLIP interface with new
specificity. In a third project I will demonstrate how engineering
Interferon for high binding affinity to its receptors altered its biological
activity in a differential manner, demonstrating the use of protein-engineering
to make more potent therapeutic proteins.
Ilan Samish
Defining the Fold Space of the Membrane Proteome
Dept of Biochemistry & Biophysics and Dept. of Chemistry University
of Pennsylvania, Philadelphia, PA, USA
Membrane
proteins with multiple transmembrane (namely polytopic) helices comprise over a quarter of all open
reading frames and are the target of most drugs. Yet, due to difficulties in
determining their structure, the number and diversity of available polytopic, helical, atomic-resolution, transmembrane-protein structures (PHATS) is
significantly lower compared to their soluble counterparts. The limited raw
structural data hinders the understanding of the unique PHATS
structure-function relationships, the related structure prediction challenge,
and membrane protein design efforts. Utilizing multi-layer filters of quality
and redundancy we created a representative dataset of available PHATS. We used
this dataset to formulate motifs at the level of sequence, super-secondary
structure, residue and atom. Complimentary, these parameterized motifs are
being incorporated into prediction and design tools as well as embedded as
building blocks within soluble proteins.
Back to top of page
Luhua Lai
From structure to systems based drug design
College of Chemistry and Molecular Engineering,
& Center for Theoretical Biology, Peking University, Beijing, China
Structural
based drug design has been widely used in drug discovery for leading compounds
identification and optimization.
Many successful applications have been reported. Various docking methods and de novo structural based drug design
programs have been developed.
However, all these methods were developed based on the assumption that
one compound binds to one target.
In fact, drugs will encounter many biological molecules in the human
body and may cause unexpected deleterious or beneficial effects. In order to understand the mechanism of
drug action, disease related molecular
networks need to be studied.
In this talk, I will introduce the Multi-Target Optimum Intervention
(MTOI) method we have developed for key targets identification and optimum
intervention strategy discovery to shift a biological network from a disease
state to a normal state. As
systems-based drug intervention often requires simultaneous control of multiple
targets, we also explored possibilities for multi-target based drug design. MTOI has been successfully used in
simulating the inflammation related arachidonic acid
metabolic network, which may be generally applicable in systems based drug
design approaches.
Haim J Wolfson
Atomic
Resolution Modeling of Large Macromolecular Assemblies
School of Computer Science, Tel Aviv University, Tel Aviv,Israel
Modelling of multimolecular
assemblies is crucial for the understanding of cellular function. Nevertheless, most of the structures in
the PDB are either monomers or dimers. The yeast cell, for example, contains
approximately 800 distinct core complexes of 5 proteins, on the average, most
of which have not yet been structurally characterized. In parallel, the various Structural
Genomics efforts and the improvement in homology modeling techniques provide a
wealth of single protein atomic resolution structures. In addition, recent developments in
experimental techniques, such as cryo-EM, FRET, SAXS
provide low resolution information on large
macromolecular complexes and distance constraints between the interacting
units. Development of efficient
algorithms, which integrate the high and low resolution
data, in order to model macromolecular complexes at atomic resolution is a key
Structural Bioinformatics task.
At
the talk we shall discuss and present several methods, which tackle the Multimolecular Assembly task by integrating experimental
protein data at different resolutions, in particular, the integration of cryo-EM and X-ray crystallography data.
K. Lasker, O. Dror, M. Shatsky, R. Nussinov, and H. Wolfson, EMatch: Discovery of High Resolution Structural Homologues
of Protein Domains in Intermediate Resolution Cryo-EM,
IEEE/ACM Trans. on Computational Biology and Bioinformatics, 4(1), 28—39,
(2007).
K. Lasker, M. Topf, A. Sali, H.J. Wolfson, Inferential optimization for fitting multiple
components into a cryoEM map of their assembly, J.
Mol. Biol. 388: 180-194, (2009).
Ron
Milo
Optimality
in Carbon Metabolism
Department of
Plant Sciences, Weizmann Institute of Science, Rehovot,
Israel
Carbon metabolism uses a complex series of enzymatic steps
to fix carbon dioxide into sugars and then convert them into metabolic
precursors. Can we gain insight into the constraints that shape evolutionÕs
solution to this task? We use a novel computational approach to generate all
possible paths between every two metabolites. We find that central metabolism
is built as a minimal walk between the twelve precursor metabolites that form
the basis for biomass: Every pair of consecutive precursors
in the network is connected by the minimal number of enzymatic steps.
Similarly, input sugars are converted into precursors by the shortest possible
enzymatic paths. This suggests an optimality principle for the structure of
central metabolism. The approach is applied to design new carbon fixation pathways which are potential alternatives to the
Calvin-Benson cycle.
Yitzhak Pilpel
Optimal translation
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, ISRAEL
Technologies to measure translation
of proteins are now rapidly emerging, transforming our understanding of the
proteome. Yet, unlike transcription research, where regulatory sequence
elements and motifs are often well characterized, in the study of translation
we are missing many of the sequence features that regulate the process and its
efficiency. In this talk I will present our attempts to fill this gap of
knowledge. Analyzing dozens of sequenced genomes we found a universally
conserved design of gene sequences that governs translation. According to the
conserved pattern, translation of genes starts by a low translation efficiency
segment, which is then followed by a longer segment of elevated level of
efficiency. We provide a model to rationalize the observed design and suggest
that it evolved and is repeatedly selected for as it optimizes the process of
protein translation and minimizes the cost of expression in cells.
Sergey Malitsky1,
Asa Eitan1, Kati Hanhineva2, Eyal Blum1, Hadar Less1,
Ilya Venger1, Yuval Eshed1, and
Asaph Aharoni1
Systems biology: integrating metabolomics
and transcriptomics
1Department of Plant Sciences, Weizmann Institute of Science, P.O. Box 26,
Rehovot 76100, Israel; 2University of
Kuopio, Department of Biosciences, Kuopio, Finland
The
production of secondary metabolites from their building blocks in
primary/central metabolism is a pricey process. These specialized substances
often accumulate in considerable concentrations either constitutively during
growth and development or in response to multiple stresses. Moreover, in some
cases these substances could only be partially recycled if at all. It is
therefore inevitable that synthesis of secondary metabolites will be tightly
linked to the availability of their major precursors in primary metabolism as
for example those containing sulfur and nitrogen. One way to maintain the
system at balance will be to utilize regulatory machineries that could
simultaneously tune the primary-secondary interface. In the study presented we
used transcriptomics and metabolomics
assays to demonstrate the coordinated transcriptional control of secondary
metabolism and their precursor pathways in primary metabolism. In one example
we show that enhancing the levels of the sulfur-containing defense compounds
(i.e. glucosinolates) requires activation of sulfur
assimilation and extensive transcriptional and metabolic induction of
structural genes and metabolites associated with primary metabolism, starting
from the TCA cycle all the way up to the committed steps of methionine
biosynthesis. In the last part of the talk new developments in the metabolomics field will be presented in which metabolic
profiling of cells isolated through Fluorescence-Activated Cell Sorting (FACS)
of specific cell layers in roots was performed.
Piotr Zielenkiewicz
Protein-protein interaction inhibitors: Application to Cystic
Fibrosis
Institute of Biochemistry and Biophysics,
Polish Academy of Sciences
Cystic
fibrosis is a lethal autosomal recessive genetic disorder correlated with abnormal Cl−
conductance at the plasma membrane of
epithelial cells, resulting in the disruption of
fluid and ion homeostasis. It is caused by defects in the cystic fibrosis transmembrane
conductance regulator (CFTR), which is also a
protein kinase A-regulated chloride ion channel.
The
most common mutation responsible for cystic fibrosis is the deletion
of residue Phe508 (ΔF508) in the first nucleotide-binding domain (NBD1). Structural and biophysical studies on
complete human NBD1 domains failed to
demonstrate significant changes of in vitro
stability or folding kinetics in the presence or
absence of the ΔF508 mutation. Crystal structures show minimal changes in protein conformation. Changes in local surface topography at the site of the mutation,
which is located in the region of NBD1
believed to interact with the first membrane spanning
domain of CFTR, are considered to be the cause
of altered interdomain interactions of the mutant
protein. However, there is another possible reason of abnormal CFTR trafficking and degradation that is to be
investigated, rather complementary than
contrary to the first one. Phenylalanine 508
interacts with surrounding amino acids, contributing to the stiffness of entire region. Although the mutant protein retains its structure in the solution, it is
possible, that the mutation slightly
destabilizes the NBD1 domain, allowing it to
cover much broader conformational space. As a result
a hydrophobic part of the protein could be exposed, inducing detection of CFTR as misfolded
and thus leading to degradation of the protein.
It will be
shown, using Molecular Dynamics simulations, that native and ΔF508 CFTR
exhibit different behaviour. In particular, the
mutant protein exposes more hydrophobic surface in a time frame allowing its
detection by housekeeping proteins. Potential inhibitors of CFTR interactions
with the housekeeping proteins, obtained from the exhaustive search of small
compound databases, will be proposed. Four
of tested small molecules efficiently allow CFTR mutant to escape from the ER
quality control system and result in appearance a functional CFTR channel in
the epithelial cell membrane.
This work was supported by the EU project
LSHG-CT-2005-512044. The results presented are significant contributions of G. Wieczorek (MD) and N.Odolczyk
(inhibitors) – both IBB PAS.
Doron Lancet
Molecular recognition
and biological evolution
Department of Molecular
Genetics, Weizmann Institute of Science, Rehovot,
Israel
Molecular
recognition is an crucial element in all biological
systems. We study one of the most elaborate examples of such recognition
– the sense of smell. In humans, ~400 olfactory receptor (OR) gene can
report millions of odors to the brain. We use high-throughput genomics (next
generation sequencing, scrutiny of the 1000 genomes project) to obtain
information on OR gene variation and evolution. Formalisms used to understand
the many-to-many recognition events in olfaction are also used to decipher the
early appearance on earth of molecular interaction networks, in ways that shed
light on lifeÕs origin.
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