This is because many of the genes and their protein products have only been predicted by computer algorithms that are at this time imperfect. The field of proteomics aims to discover all the proteins produced by a given organism.
Such a proteome map would bring the possibility of deducing the precise number, and location in the genome, of the genes coding for proteins. This is much more complex than simply mapping the genome from end to end because it involves detecting all proteins even though some are present only in very small amounts, while some are confined to specific organs and/or are only synthesised at certain times or stages of an organism's life.
However a recent workshop supported by the European Science Foundation (ESF) concluded that it is now feasible to map at least nearly the whole proteome (the sum total of all proteins) of an organism. Such an extensive map will be an essential base for the development and eventually the widespread application of a new generation of proteomics technologies that are faster, more sensitive and more reliable than the present methods. These technologies, in turn, thanks to their improved performance could greatly improve understanding of many diseases and lead to new therapies, according to the ESF workshop's coordinator Professor Rudolf Aebersold from Institute of Molecular Systems Biology in Switerzland. Most diseases, including cancer and many pathogenic infections, involve disruption to regulatory processes in cells or tissues with associated changes in the abundance of proteins and their interactions, Aebersold pointed out.
"The idea would be that if we could map out the whole proteome, we could develop a toolbox structure enabling assays (for detecting proteins) to be done faster and more cheaply." It would then be possible to identify proteins implicated in a particular disease more readily, helping both with research into underlying causes, and ultimately in diagnosis.
Mapping the proteome will also help resolve one of biology's more recent puzzles, which is why all organisms, from the simplest to the most complex, contain a significantly higher number of predicted protein coding genes than experimentally detected proteins. The shortfall is significant - in almost all organisms there are only about 65 per cent as many proteins as had been predicted through analysis of the genome.
This is a surprise because each gene had been understood to code for a protein on a one-to-one basis. As Aebersold pointed out, there are several possible explanations for this apparent anomaly. The simplest explanation is simply a lack of sensitivity of proteomics methods, which may as a result have failed so far to identify specific classes of proteins. However given the increasing sensitivity of proteomics methods, this explanation is increasingly unlikely.
Another possibility is that there are not as many coding genes as had been thought. The number has not yet been reliably counted, and is currently estimated by computer predictions based on knowledge of the sequence structure of genes already known. Another possibility is that there are as many genes as had been thought, but either that a substantial number code for proteins that are only very rarely or under specific conditions expressed in cells or tissues, or that the mRNA, which is the intermediate product between the DNA of the genome and the proteins, is not translated into the final protein product.
Aebersold hopes that the workshop will lead to a major EU-funded project to map complete proteomes, answer some of these questions, and arrive at a more accurate count of how many genes there are in humans and other organisms. "If something can be identified as a protein, that's the most direct evidence we can have that a gene really exists," said Aebersold.
It will though be hard to tell when the job is done, because the proteome, unlike the genome, is not a stable, defined physical entity. While the genome comprises the famous double helix of DNA that can be physically sequenced on an end-to-end basis, the proteome is simply the total of all proteins, and so by definition you can never be absolutely sure the last one has been found, given that some are present intermittently or in small amounts and can easily be missed during analysis. Mass spectrometry is used to perform this analysis and identify proteins in complex samples, after applying some technique such as chromatography to separate out the individual proteins. The amino acid sequence of each protein can be determined after separation, from the relationship between electric charge and mass.
As Aebersold noted, the biggest prize of proteomics will be a much simpler and efficient technique for identifying individual proteins within samples, which could eventually have huge diagnostic power as well as application in research and across the whole field of biotechnology and pharmacology. The ESF workshop has prepared the ground by helping establish the collaborative framework for Europe to participate fully in the great proteomics initiative, and now it is up to the EU to provide the funding.
The workshop Model Organism Proteomics, which was one of the series of events organised by the ESF Exploratory Workshops, was held 11-13 April 2007, in Zurich, Switzerland. Delegates were given a thorough overview of the state of the field and Europe's place in it, with details of various successful collaborations. Following the workshop, Europe is much better placed to harness its resources in the field effectively.
Each year, ESF supports approximately 50 Exploratory Workshops across all scientific domains. These small, interactive group sessions are aimed at opening up new directions in research to explore new fields with a potential impact on developments in science.
Thomas Lau | alfa
Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden
The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie
Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.
A warming planet
Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.
The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...
Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...
Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!
When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...
For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.
Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...
19.09.2017 | Event News
12.09.2017 | Event News
06.09.2017 | Event News
22.09.2017 | Life Sciences
22.09.2017 | Medical Engineering
22.09.2017 | Physics and Astronomy