MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize

Abstract

An extensive search for maize (Zea mays) genes involved in cell wall biosynthesis and assembly has been performed and 735 sequences have been centralized in a database, MAIZEWALL (http://www.polebio.scsv.ups-tlse.fr/MAIZEWALL). MAIZEWALL contains a bioinformatic analysis for each entry and gene expression data that are accessible via a user-friendly interface. A maize cell wall macroarray composed of a gene-specific tag for each entry was also constructed to monitor global cell wall-related gene expression in different organs and during internode development. By using this macroarray, we identified sets of genes that exhibit organ and internode-stage preferential expression profiles. These data provide a comprehensive fingerprint of cell wall-related gene expression throughout the maize plant. Moreover, an in-depth examination of genes involved in lignin biosynthesis coupled to biochemical and cytological data from different organs and stages of internode development has also been undertaken. These results allow us to trace spatially and developmentally regulated, putative preferential routes of monolignol biosynthesis involving specific gene family members and suggest that, although all of the gene families of the currently accepted monolignol biosynthetic pathway are conserved in maize, there are subtle differences in family size and a high degree of complexity in spatial expression patterns. These differences are in keeping with the diversity of lignified cell types throughout the maize plant.

Figure 1.

Schematic view of the strategy and content of the cell wall gene catalog found in MAIZEWALL.

Figure 2.

Structure of the MAIZEWALL database. Each box represents a different Web page. Arrows indicate links between pages.

Figure 3.

Characterization of the PAL gene family in maize. A, Phylogenetic analysis. Classes were defined according to evolutionary distances defined by Phylip 3.5 software. B, Gene expression in organs at the four- to five-leaf stage and IN1 and IN6 at silking. Values indicate the normalized signal hybridization intensity for each gene and (−) signifies a below-background signal intensity of ≤6,000. C, Relative contribution of each gene to total PAL gene expression. R, Roots; L, leaves, YS, young stems, which results from piled-up internodes at the four- to five-leaf stage. IN6, Internode just below the node bearing the ear at silking; IN1, basal internode at silking. Note that equivalent datasets as found in B and C are available for all gene entries in MAIZEWALL.

Figure 4.

Characterization of the 4CL gene family in maize. A, Phylogenetic analysis. Classes were defined according to evolutionary distances defined by Phylip 3.5 software. Contig numbers 2448387.2.1 and 17163.2.2 annotated as 4CL-like; contig numbers 3106166.2.1 and 1716323.2.1 annotated as putative 4CL. For 4CL2, a contig was not found in the GPI databases. B, Gene expression in organs at the four- to five-leaf stage and internodes at different developmental stages. Values indicate the normalized signal hybridization intensity for each gene and (−) signifies a below-background signal intensity of ≤6,000. Note that contig numbers 1716323.2.2 and 2448387.2.1 were not included in expression studies because we were unable to amplify corresponding GSTs. C, Relative contribution of each gene to total 4CL gene expression. R, Roots; L, leaves; YS, young stems, which results from piled-up internodes at the four- to five-leaf stage. IN6, Internode just below the node bearing the ear at silking; IN1, basal internode at silking. Note that equivalent datasets as found in B and C are available for all gene entries in MAIZEWALL.

Figure 5.

Characterization of the CCoAOMT gene family in maize. A, Phylogenetic analysis. Classes were defined according to evolutionary distances defined by Phylip 3.5 software. Contig numbers 2591258.2.1, 2430769.2.1, and 2943966.2.1 annotated as putative CCoAOMT. B, Gene expression in organs at the four- to five-leaf stage and internodes at different developmental stages. Values indicate the normalized signal hybridization intensity for each gene. C, Relative contribution of each gene to total CCoAOMT gene expression. R, Roots; L, leaves; YS, young stems, which results from piled-up internodes at the four- to five-leaf stage. IN6, Internode just below the node bearing the ear at silking; IN1, basal internode at silking. Note that equivalent datasets as found in B and C are available for all gene entries in MAIZEWALL.

Figure 6.

Characterization of the CCR gene family in maize. A, Phylogenetic analysis. Classes were defined according to evolutionary distances defined by Phylip 3.5 software. Contig numbers 131555.2.2, 4695478.2.1, 2969912.2.1, 3230260.2.1, and 131555.2.3 annotated as putative CCRs. For CCR2, a contig was not found in the GPI database. B, Gene expression in organs at the four- to five-leaf stage and internodes at different developmental stages. Values indicate the normalized signal hybridization intensity for each gene and (−) signifies a below-background signal intensity of ≤6,000. C, Relative contribution of each gene to total CCR gene expression. R, Roots; L, leaves; YS, young stems, which results from piled-up internodes at the four- to five-leaf stage. IN6, Internode just below the node bearing the ear at silking; IN1, basal internode at silking. Note that equivalent datasets as found in B and C are available for all gene entries in MAIZEWALL.

Figure 7.

Characterization of the CAD gene family in maize. A, Phylogenetic analysis. Classes were defined according to evolutionary distances defined by Phylip 3.5 software. Note that contig number 2485944.3.1 was annotated putative CAD, contigs numbers 3203838.2.1 and 4424417.2.1 were annotated SAD-like, and contig numbers 3071507.2.1 and 2949673.2.1 were annotated SAD. B, Gene expression in organs at the four- to five-leaf stage and internodes at different developmental stages. The values indicate the signal-normalized hybridization intensity for each gene and (−) signifies a below-background signal intensity of ≤6,000. Note that contig number 2949673.2.1 was not included in CAD expression studies because we were unable to amplify a corresponding GST. C, Relative contribution of each gene to total CAD gene expression. R, Roots; L, leaves; YS, young stems, which results from piled-up internodes at the four- to five-leaf stage. IN6, Internode just below the node bearing the ear at silking; IN1; basal internode at silking. Note that equivalent datasets as found in B and C are available for all gene entries in MAIZEWALL.

Figure 8.

Histochemical localization of lignin in maize organs at the four- to five-leaf stage and internodes at different stages of development at silking. Sections were stained with Maüle reagent. A to C, Transverse sections of primary roots. A, Overall view of a root section. Red-purple staining in the cells of the hypodermal layers and vascular cylinder indicates the presence of S-unit lignin. B, Close-up of hypodermal layers. The three innermost cell layers stained red-purple and the outermost layer just below the epidermis is stained brown, indicating G-unit lignin (large arrow). C, Close-up of the vascular cylinder. The Casparian strip of the endodermis and two rows of xylem vessels embedded in parenchyma cells are all stained red-purple. d to G, Transverse sections in leaves. D, Leaf blade. E, Midrib. F, Close-up of a vascular bundle from a large vein in the blade. G, Close-up of a vascular bundle from a large vein in the midrib. In all cases, note the yellow-brown coloration of the sclerenchyma cells above the vascular bundle, indicating the absence of S-unit lignin. H, Longitudinal section through the young stem, resulting from piled-up internodes of plants at the four- to five-leaf stage. Black lines indicate the positions of transverse sections in internodal and nodal regions shown in I and J, respectively. I, Transverse section in the first internode. J, Transverse section in the node. Only walls of the protoxylem are stained red. K, General view of a maize plant at the silking stage grown under greenhouse conditions. White lines indicate the positions of transverse sections of IN1 and IN6 shown in L and M, respectively. L, Transverse sections of IN1 showing red staining of all lignified tissues, including sclerenchyma, parenchyma cells, and xylem. M, Transverse sections in IN6. Note that sclerenchyma cells are very weakly stained and parenchyma cells are not at all. en, Endodermis; ph, phloem; p, pith; ep, epidermal cells; hp, hypodermal cell; c, cortex; s, sclerenchyma; x, xylem; lv, large veins; sv, small veins; vb, vascular bundle; lp, lignified parenchyma; px, protoxylem; mx, metaxylem. Magnification bars: B, C, and F, 100 μm; A, D, E, G, L, and M, 200 μm; I and J, 400 μm.