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Expression Data Leads to Identification of Arabidopsis Root Growth Gene

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Alterations in an Arabidopsis transcription factor gene tied to reactive oxygen species levels in the plant's roots leads to more robust root growth, a Duke University team reported online today in Cell.

While searching for genes involved in the transition from cellular proliferation to differentiation in Arabidopsis roots, the researchers found UPB1, a transcription factor that regulates a group of peroxidase enzymes. Mutating the gene produced changes in cell proliferation in Arabidopsis roots — apparently due to downstream effects on reactive oxygen species that are regulated by peroxidases.

"Our microarray expression analysis coupled with UPB1 ChIP-chip analysis indicated that UPB1 directly represses a set of peroxidases as cells begin to differentiate," senior author Philip Benfey, director of the Duke Institute for Genome Sciences & Policy's Center for Systems Biology, and his co-authors wrote.

These and other results "provided strong evidence that these peroxidases control [reactive oxygen species] distribution, which in turn governs the transition from proliferation to differentiation," they added.

Benfey is CEO and co-founder of a Duke University spin out called GrassRoots Biotechnology. The company, which started in 2007, has an eye toward biofuel technology and carbon sequestration and has reportedly applied for patents related to the new findings.

The researchers initially identified the root growth-related transcription factor by sifting through RootMap gene expression datasets generated for a 2007 study by Benfey and others, looking for expression patterns linked to the shift from proliferation to differentiation in Arabidopsis roots.

"We systematically looked for those genes that come 'on' precisely when cells transition from proliferation to differentiation and then turn 'off' again just as quickly," Benfey said in a statement.

In the process, they found roughly 100 transcription factor genes that are more highly expressed in a root region in and around the elongation zone. Using insertional mutant Arabidopsis lines, they then looked at whether they could find changes in root growth in a set of plants in which 96 of the genes were individually mutated.

Indeed, the team found root changes in an Arabidopsis line containing an insertion in an uncharacterized gene called At2g47270 that apparently belongs to a basic helix-loop-helix or bHLH domain-containing family of transcription factors.

Plants with expression-curbing mutations in the gene, which they dubbed UPBEAT1 or UPB1, had longer roots containing more so-called cortex cells. On the other hand, bumping up the transcription factor's expression produced roots with shorter roots and fewer cortex cells.

Meanwhile, the team's results from gene expression experiments on wild type and UPB1 mutant plants — as well as ChIP-chip experiments using an Agilent custom long oligonucleotide Arabidopsis promoter array — indicated that the transcription factor regulates genes coding for a set of peroxidases in the elongation zone of roots.

The peroxidase enzymes, in turn, are known to tweak the levels of reactive oxygen species such as hydrogen peroxide and superoxide in an area of the root straddling the elongation zone and meristematic zone, the researchers explained. Plants with a mutated version of UPB1 showed elevated expression of three peroxidase genes as well as increased superoxide and decreased hydrogen peroxide levels in the elongation zone of roots.

Increased expression of the transcription factor, on the other hand, decreased expression of the peroxidase genes and curbed superoxide levels, but increased hydrogen peroxide levels. Similarly, the researchers found that they could influence root growth by directly altering reactive oxygen species levels or peroxidase activity.

Based on their findings, the team concluded that elevated superoxide levels stimulate root proliferation, while hydrogen peroxide contributes to root differentiation.

Because UPB1 apparently influences the levels of these reactive oxygen species through a mechanism distinct from plant hormone signaling pathways, they explained, it may be possible to alter root growth by specifically targeting the gene — a strategy that may prove useful for those developing biofuel crop plants.

"[B]iofuel crops usually can't be harvested until the second or third year," Benfey said in a statement. "A method to improve root growth could have a major role in reducing the time to harvest for warm season grasses."

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