Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Getting round gene loss

01.11.2010
A naturally occurring back-up system in plants to produce metabolites compensates for experimentally induced gene loss

Genes ‘knocked out’ experimentally in metabolic networks of the model plant species, Arabidopsis thaliana, are compensated for by duplicate genes or alternative synthetic pathways, according to research led by Kousuke Hanada of the RIKEN Plant Science Center, Yokohama1.

Gene knockouts often have no obvious effects on an organism’s biological characteristics or ‘phenotype’, because their function is compensated for by duplicate genes or alternative pathways allow the effects of gene loss to be circumvented.

For metabolic products, studies on these mechanisms have been limited to yeast. Hanada’s team therefore assessed the relative importance of these mechanisms in Arabidopsis. “Arabidopsis suited our purposes beautifully because many gene knockout mutants have been generated and many of its metabolic networks are known,” explains Hanada.

To study the robustness of Arabidopsis metabolic networks to gene loss the researchers knocked out individually some 2,000 highly expressed genes and then quantified 35 metabolic products in the seeds of the mutant plants by high-throughput analysis.

They compared what happened to production of metabolites when genes with and without duplicates were knocked out. The metabolites assessed included 17 essential amino acids (primary metabolites) found in all organisms, and 18 secondary metabolites called glucosinolates produced specifically by Arabidopsis and its relatives.

Knocking out either single-copy genes or genes with only distantly related ‘duplicates’ tended to have larger metabolic effects than those caused by knocking out genes having closer copies resulting from more recent gene duplication events. “Only recently duplicated genes appear to play a significant role in functional compensation of metabolites in Arabidopsis,” says Hanada.

By analyzing the structure of the Arabidopsis metabolic network, the researchers found that primary metabolites are more often synthesized by alternative biochemical pathways than are secondary metabolites.

Primary metabolites are more likely than secondary metabolites to be essential for plant survival. Surprisingly, however, the researchers found that duplicate genes more often compensated functionally for experimentally induced gene loss in the synthesis of secondary metabolites than in that of primary metabolites. This contrasted with their previous work that showed that, in general, more severe phenotypic effects in Arabidopsis tend to be better compensated for by gene duplication than less severe effects2.

Hanada suggests that the existence of multiple alternative pathways for synthesizing primary metabolites makes these particular Arabidopsis networks highly robust to the loss of individual genes.

“Our findings shed valuable new light on the gene–phenotype relationship, laying the groundwork for new theoretical models in systems biology,” says Hanada.

The corresponding author for this highlight is based at the Gene Discovery Research Group, RIKEN Plant Science CenterJournal information

1. Hanada, K., Sawada, Y., Kuromori, T., Klausnitzer, R., Saito, K., Toyoda, T., Shinozaki, K., Li, W-H. & Hirai, M.Y. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Molecular Biology and Evolution Advance Access, published 24 August 2010 (doi: 10.1093/molbev/msq204).

2. Hanada, K., Kuromori, T., Myoga, F., Toyoda, T., Li, W-H. & Shinozaki, K. Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biology and Evolution 1, 409–414 (2009).

gro-pr | Research asia research news
Further information:
http://www.rikenresearch.riken.jp/eng/research/6433
http://www.researchsea.com

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>