Bacteria are some of the simplest forms of life and have been studied by scientists trying to identify the smallest collection of genes – or minimal genome – that is needed for maintaining life.
Traditionally scientists have done this by removing, or ‘knocking out’, a series of individual genes from a bacterial genome to see what effect this has on its ability to survive.
They can then infer which genes are essential to the organism, and which are not, to work out which are needed for the minimal genome.
However this knock out approach wrongly removes many of the genes that are essential to the survival of bacteria, according to researchers from Heidelberg (Germany), Manchester (UK), Budapest (Hungary) and Bath (UK).
The researchers made this discovery after developing a new approach to genome modelling which, given the organism’s evolutionary history and knowledge of its surrounding environment, allows them to predict which genes a bacterium’s genome should contain.
“Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.
“This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.
“When you knock out one gene, the genome can compensate by using an alternative gene.
“But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.
“Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.
“In fact, because there are alternative pathways to the same product, by removing either of the genes you make the other essential for survival; each gene deletion reduces the available space for further reduction of the genome.
”Including these alternative pathways into the minimal genome almost doubles its size.”
The researchers have developed a way of predicting bacterial genome content using two bacteria that have evolved from E.coli.
Buchnera and Wigglesworthia live inside insects in a symbiotic relationship where they provide essential molecules for their hosts in return for essential basic foods.
Since evolving from E.coli, the Buchnera and Wigglesworthia genomes have lost some of the genes that they would otherwise need for survival.
Using computer modelling and knowledge of the present day ecology of the bacteria the researchers were able to model this process of gene loss.
They accurately predicted about 80 per cent of the gene content of the two bacteria, including some of the non-obvious features of their genomes.
“Far from being a cause for disease, the insects need these bacteria to supply them with essential nutrients,” said Professor Hurst.
“In these relatively cosy conditions, Buchnera and Wigglesworthia have lost some of the genes they would otherwise need to produce some of the basic molecules they need to survive.
“Being able to predict the content of a genome based on the ecology of an organism is useful because we could potentially use it to predict gene content at different stages of an organism’s evolution.
“This will help us understand more about how the genome of different organisms have evolved over long periods of time and should also inform attempts by experimentalists to construct minimal genomes by gradual evolution in the laboratory.”
Similar methods might also be used to build a blueprint of a bacterium with desired metabolic properties, for example identifying which genes would a bacterium need to efficiently digest specific waste chemicals.
The research has been supported by the Hungarian Scientific Research Fund, EMBO, the Human Frontier Science Program, DFG and the Biotechnology and Biological Sciences Research Council.
’Chance and necessity in the evolution of minimal metabolic networks’ will be published in Nature on 30 March 2006.
Andrew McLaughlin | alfa
Bacteria as pacemaker for the intestine
22.11.2017 | Christian-Albrechts-Universität zu Kiel
Researchers identify how bacterium survives in oxygen-poor environments
22.11.2017 | Columbia University
The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.
Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....
The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.
Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...
Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.
That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...
Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.
During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....
The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.
Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...
15.11.2017 | Event News
15.11.2017 | Event News
30.10.2017 | Event News
22.11.2017 | Business and Finance
22.11.2017 | Physics and Astronomy
22.11.2017 | Physics and Astronomy