Plant genes that are part of the same biological process maintain the same gene "switches"

Nicole Marie Creux¹, Martin Ranik¹, David Kenneth Berger², Alexander Andrew Myburg¹
1Department of Genetics, 2Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

Summary

A stretch of DNA harbours many genes and these genes dictate the protein or enzyme structures and functions within a cell. While genes make up a large component of the cell’s DNA, there are non-coding regions of DNA such as the promoters of these genes that have received less attention until recently. Promoters are the regions of DNA that control the expression of genes. Promoters can be divided into two parts; the region closest to the gene is often referred to as the proximal promoter. The proximal promoter acts as the “on/off” switch of the gene and initiates the production of the necessary cell components. The second part of the gene’s promoter is known as the distal promoter. This region of DNA is located next to the proximal promoter but further away from the gene and acts as the “dimmer switch” of the gene. The distal promoter controls where, when and at which levels the gene is expressed. Both the proximal and distal promoters contain small “codes” within them that make this stringent form of regulation possible. These “codes” are very short stretches of DNA sequence, usually between 6-8 base pairs in length, which are referred to as cis-regulatory elements. Cis-regulatory elements are so important to the functioning of the genes that there is evidence that these elements are conserved in genes with the same function, even among distantly related organisms. At any given time an organism has a large number of different genes that function at the same time to keep just one biological process in the cell running smoothly. The theory states that because all these genes need to be expressed at the same time they should share the same cis-regulatory elements.

Figure 1. An example of the cis-elements highlighted by this study (for a full representation see the full article). The horizontal black lines represent the individual promoters of the study. The scale in number of base pairs upstream of the transcriptional startsite is indicated at the top. The promoters are separated into two sets with the one set containing promoters associated with primary cell wall formation and a secondary set associated with secondary cell wall formation. Within each set the orthologous promoters are grouped together (groups A- F). The motif sequence logos on the right were obtained from MotifSampler and the light and dark purple blocks indicate where and in which promoters these elements were identified in.

Figure 2. Eucalyptus CesA promoter activity in Arabidopsis. Ubiquitous GUS expression driven by the EgCesA4 and 5 promoters is evident in Arabidopsis leaf blades (a, b and d), flowers (c), trichomes (e) and seedlings (f). GUS expression driven by the EgCesA1 (g, h, i) and EgCesA3 (j, k) promoters in Arabidopsis thaliana plants. Expression is evident in secondary xylem of stems (g, h), leaf veins (i) and seedling (k) as well as root vasculature (j). Lack of GUS staining is evident in non-vein tissues of seedlings (k).

In this study we isolated functional promoters (Figure 1) of six forest tree (Eucalyptus) genes and a survey of the possible shared cis-regulatory elements (“dimmer switches”) in these promoters was performed (Figure 2). The six genes on which this study focused were members of the cellulose synthase (CesA) gene family. Cellulose synthase is a complex of proteins that are situated in the plants cell membrane. The cellulose synthase proteins are responsible for the production and deposition of cellulose in the plant cell wall. Cellulose is produced by all plants and is deposited in the plant’s cell wall. The deposition of cellulose in the plant’s cell wall gives the plant cell strength and protects it from invading pathogens. Cellulose is also used by the plant to reinforce the cells which carry the water from the roots to the shoot tips. These water-carrying cells (xylem cells) are placed under tremendous pressure as they fight against gravity to get the water to the shoot tips. The taller the plant the more force is placed on these cells and so the cells need to be stronger. Thus, trees have thick, hardened ‘stems’ (trunks), their plant cells have very thick cell walls in order to cope with the pressures and these cell walls are reinforced predominantly with cellulose. Therefore, cellulose is an important biopolymer to plants and forms the basis of a number of industries because it is the main component of wood. Today, with the strong focus on environmentally friendly fuels, cellulose is even more important as it can be fermented to produce cellulosic ethanol, which is a main component of “green” fuels. Once thoroughly tested some of the cis-regulatory elements identified in this study can be used to enhance cellulose production in the trees by constructing synthetic (man-made) promoters, but there is still a great deal of testing that must be performed before this can be a reality. Increasing the amount of cellulose produced per tree could positively influence a number of sectors including the environment and the economy.

Related Articles

• Creux, N. M., Ranik, M et al. (2008). Comparative analysis of orthologous cellulose synthase promoters from Arabidopsis, Populus and Eucalyptus: evidence of conserved regulatory elements in angiosperms. New Phytologist 179:722-737.