Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Getting round gene loss

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:

More articles from Life Sciences:

nachricht Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München

nachricht Second research flight into zero gravity
21.10.2016 | Universität Zürich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

Im Focus: Ultra-thin ferroelectric material for next-generation electronics

'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.

Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Resolving the mystery of preeclampsia

21.10.2016 | Health and Medicine

Stanford researchers create new special-purpose computer that may someday save us billions

21.10.2016 | Information Technology

From ancient fossils to future cars

21.10.2016 | Materials Sciences

More VideoLinks >>>