Annals of Botany

Study of submergence shows that small is beautiful

It is fascinating to see how the basic tenets of molecular biology have been modified over the past 30 years and, in particular, the discovery that different types of RNA act in the regulation of gene expression. The rise to prominence of microRNA (miRNA), a class of RNA that targets mRNA for degradation, has been especially spectacular. The first miRNA was discovered in 1993 but it was not until 2000 that a second was found. However, since then, the list has grown to several thousand (see http://microrna.sanger.ac.uk). In plants they are involved in regulation of gene expression in a range of developmentally or environmentally induced events. This picture has been added to by the work of Zhang et al. (Baoding, Wuhan and Jingzhou, China, pp. 509–519). They used a miRNA microarray to investigate miRNA populations in maize roots, showing that expression of 39 different miRNAs is affected by submergence, falling into four different patterns. A group of five miRNAs show early up-regulation; the target mRNAs for four of these encode transcription factors. Thus these transcription factors, mostly involved in root growth and morphogenesis, are in turn down-regulated, most likely leading to an inhibition of elongation and a promotion of adventitious roots. A fifth early up-regulated miRNA targets starch synthase and aminotransferase mRNAs, leading to reduction in starch and amino acid synthesis. The latter is reciprocated by the second pattern of miRNA changes in which down-regulation occurs in the first 24 hours, followed by a later re-induction of synthesis. The target messenger RNAs of these miRNAs thus show early up-regulation. They include mRNAs encoding transcription factors and enzymes involved in polysaccharide breakdown and enzymes involved in eliminating the products of anaerobic metabolism. The overall pattern of changes is thus seen to enable the root to respond appropriately to submergence at all levels from morphogenetic to metabolic.