Getting around gene loss

Oct 29, 2010
Figure 1: In the plant, Arabidopsis thaliana, which is commonly used as an experimental model, duplicate genes or alternative synthetic pathways make the plant robust against the deletion of highly expressed genes. Credit: 2010 iStockphoto/pkujiahe

Genes ‘knocked out’ experimentally in metabolic networks of the model plant species, Arabidopsis thaliana (Fig. 1), are compensated for by duplicate genes or alternative synthetic pathways, according to research led by Kousuke Hanada of the RIKEN Plant Science Center, Yokohama.

Gene knockouts often have no obvious effects on an organism’s biological characteristics or ‘phenotype’, because their function is compensated for by duplicate 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 , 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 effects.

Hanada suggests that the existence of multiple alternative pathways for synthesizing primary 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.

Explore further: How an RNA gene silences a whole chromosome

More information:
Hanada, K., et al. 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

Hanada, K., et al. Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis. Genome Biology and Evolution 1, 409–414 (2009) article .

Related Stories

Computer predicts anti-cancer molecules

Jun 17, 2008

A new computer-based method of analyzing cellular activity has correctly predicted the anti-tumour activity of several molecules. Research published today in BioMed Central's open access journal Molecular Cancer describes 'CoMet ...

The 21st century tomato

Jun 28, 2008

When tomatoes ripen in our gardens, we watch them turn gradually from hard, green globules to brightly colored, aromatic, and tasty fruits. This familiar and seemingly commonplace transformation masks a seething mass of components ...

Plant gene clusters for natural products

Mar 20, 2008

John Innes Centre scientists have found that plants may cluster the genes needed to make defence chemicals. Their findings may provide a way to discover new natural plant products of use as drugs, herbicides ...

Recommended for you

How an RNA gene silences a whole chromosome

38 minutes ago

Researchers at Caltech have discovered how an abundant class of RNA genes, called long non-coding RNAs (lncRNAs, pronounced link RNAs) can regulate key genes. By studying an important lncRNA, called Xist, ...

Single cells seen in unprecedented detail

2 hours ago

Researchers have developed a large-scale sequencing technique called Genome and Transcriptome Sequencing (G&T-seq) that reveals, simultaneously, the unique genome sequence of a single cell and the activity ...

York's anti-malarial plant given Chinese approval

Apr 24, 2015

A new hybrid plant used in anti-malarial drug production, developed by scientists at the University of York's Centre for Novel Agricultural Products (CNAP), is now registered as a new variety in China.

The appeal of being anti-GMO

Apr 24, 2015

A team of Belgian philosophers and plant biotechnologists have turned to cognitive science to explain why opposition to genetically modified organisms (GMOs) has become so widespread, despite positive contributions ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.