Primary phloem-specific expression of a Zinnia elegans homeobox gene

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks

BACKGROUND

Uncovering the complex transcriptional regulatory networks (TRNs) that underlie plant and animal development remains a challenge. However, a vast amount of data from public microarray experiments is available, which can be subject to inference algorithms in order to recover reliable TRN architectures.

RESULTS

In this study we present a simple bioinformatics methodology that uses public, carefully curated microarray data and the mutual information algorithm ARACNe in order to obtain a database of transcriptional interactions. We used data from Arabidopsis thaliana root samples to show that the transcriptional regulatory networks derived from this database successfully recover previously identified root transcriptional modules and to propose new transcription factors for the SHORT ROOT/SCARECROW and PLETHORA pathways. We further show that these networks are a powerful tool to integrate and analyze high-throughput expression data, as exemplified by our analysis of a SHORT ROOT induction time-course microarray dataset, and are a reliable source for the prediction of novel root gene functions. In particular, we used our database to predict novel genes involved in root secondary cell-wall synthesis and identified the MADS-box TF XAL1/AGL12 as an unexpected participant in this process.

CONCLUSIONS

This study demonstrates that network inference using carefully curated microarray data yields reliable TRN architectures. In contrast to previous efforts to obtain root TRNs, that have focused on particular functional modules or tissues, our root transcriptional interactions provide an overview of the transcriptional pathways present in Arabidopsis thaliana roots and will likely yield a plethora of novel hypotheses to be tested experimentally.

Multiple cis-regulatory elements are involved in the complex regulation of the sieve element-specific MtSEO-F1 promoter from Medicago truncatula

The sieve element occlusion (SEO) gene family includes several members that are expressed specifically in immature sieve elements (SEs) in the developing phloem of dicotyledonous plants. To determine how this restricted expression profile is achieved, we analysed the SE-specific Medicago truncatula SEO-F1 promoter (PMtSEO-F1) by constructing deletion, substitution and hybrid constructs and testing them in transgenic tobacco plants using green fluorescent protein as a reporter. This revealed four promoter regions, each containing cis-regulatory elements that activate transcription in SEs. One of these segments also contained sufficient information to suppress PMtSEO-F1 transcription in the phloem companion cells (CCs). Subsequent in silico analysis revealed several candidate cis-regulatory elements that PMtSEO-F1 shares with other SEO promoters. These putative sieve element boxes (PSE boxes) are promising candidates for cis-regulatory elements controlling the SE-specific expression of PMtSEO-F1.

Transcriptional regulation in wood formation

Wood (i.e. xylem tissue) in trees is mainly composed of two types of cells, fibres and tracheary elements. Recent molecular studies of various trees, as well as the non-tree species Arabidopsis thaliana and Zinnia elegans, have revealed coordinated gene expression during differentiation of these cells in wood and the presence of several transcription factors that might govern the complex networks of transcriptional regulation. This article reviews recent findings concerning the regulation of genes by transcription factors involved in wood formation such as AUXIN RESPONSE FACTOR (ARF), CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII), KANADI (KAN), MYB and NAM/ATAF/CUC (NAC).

Isolation and characterization of a novel peroxidase gene ZPO-C whose expression and function are closely associated with lignification during tracheary element differentiation

In an attempt to elucidate the regulatory mechanism of vessel lignification, we isolated ZPO-C, a novel peroxidase gene of Zinnia elegans that is expressed specifically in differentiating tracheary elements (TEs). The ZPO-C transcript was shown to accumulate transiently at the time of secondary wall thickening of TEs in xylogenic culture of Zinnia cells. In situ hybridization indicated specific accumulation of the ZPO-C transcript in immature vessels in Zinnia seedlings. Immunohistochemical analysis using anti-ZPO-C antibody showed that the ZPO-C protein is abundant in TEs, especially at their secondary walls. For enzymatic characterization of ZPO-C, 6 x His-tagged ZPO-C was produced in tobacco cultured cells and purified. The ZPO-C:6 x His protein had a peroxidase activity preferring sinapyl alcohol as well as coniferyl alcohol as a substrate, with a narrow pH optimum around 5.25. The peroxidase activity required calcium ion and was elevated by increasing Ca2+ concentration in the range of 0-10 mM. An Arabidopsis homolog of ZPO-C, At5g51890, was examined for expression patterns with transgenic plants carrying a yellow fluorescent protein (YFP) gene under the control of the At5g51890 promoter. The YFP fluorescence localization demonstrated vessel-specific expression of At5g51890 in the Arabidopsis roots. Taken collectively, our results strongly suggest that ZPO-C and its homologs play an important role in lignification of secondary cell walls in differentiating TEs.

Transcription switches for protoxylem and metaxylem vessel formation

Land plants evolved xylem vessels to conduct water and nutrients, and to support the plant. Microarray analysis with a newly established Arabidopsis in vitro xylem vessel element formation system and promoter analysis revealed the possible involvement of some plant-specific NAC-domain transcription factors in xylem formation. VASCULAR-RELATED NAC-DOMAIN6 (VND6) and VND7 can induce transdifferentiation of various cells into metaxylem- and protoxylem-like vessel elements, respectively, in Arabidopsis and poplar. A dominant repression of VND6 and VND7 specifically inhibits metaxylem and protoxylem vessel formation in roots, respectively. These findings suggest that these genes are transcription switches for plant metaxylem and protoxylem vessel formation.

Cloning and characterization of an HDZip I gene GmHZ1 from soybean

By using cDNA-AFLP, we analyzed a recombinant inbred line population of soybean that was derived from a soybean mosaic virus (SMV) resistant cultivar Kefeng No.1 and a susceptible cultivar Nannong 1138-2. One hundred and eight fragments showing polymorphism between SMV resistant and susceptible pools were identified. One fragment w27 was 96 bp in length and showed homology to homeobox ggth with a coding region of 738 bp, encoding a protein of 245 amino acids. The genomic sequence analysis defined an intron of 521 bp in the coding region. GmHZ1 was characterized by the presence of a homeodomain (HD) with a closely linked leucine zipper motif (Zip). Southern blot analysis indicated that there was a single copy of GmHZ1 in the soybean genome. When inoculated with SMV strain N3, resistant and susceptible varieties showed reduced and increased expression of the GmHZ1, respectively. The fusion protein of GmHZ1 with GFP was targeted only in nucleus. Yeast two hybrid studies revealed that the GmHZ1 had transcriptional activation activity and can form homodimer. GmHZ1 can bind two 9-bp pseudopalindromic elements (CAAT(A/T)ATTG and CAAT(C/G)ATTG) with different affinity. Using GUS as a reporter gene, GmHZ1 was proved to be a transcriptional activator and enhanced GUS expression by binding with the two elements in plant cells. These results indicate that the GmHZ1 may have a transcriptional activator function in plant response to SMV infection.

Pattern formation in the vascular system of monocot and dicot plant species

Plant vascular tissues are organised in continuous strands, the longitudinal and radial patterns of which are intimately linked to the signals that direct plant architecture as a whole. Therefore, understanding the mechanisms underlying vascular tissue patterning is expected to shed light on patterning events beyond those that organise the vascular system, and thus represents a central issue in plant developmental biology. A number of recent advances, reviewed here, are leading to a more precise definition of the signals that control the formation of vascular tissues and their integration into a larger organismal context. Contents Summary 209 I. Introduction 209 II. The plant vascular system 210 III. Ontogeny of the vascular tissues 210 IV. Procambium development 210 V. The organisation of the vascular tissues 212 VI. The regulation of longitudinal vascular pattern formation 214 VII. The regulation of radial vascular pattern formation 220 VIII. Genetic screens for vascular development mutants 231 IX. Genes involved in vascular development identified through reverse genetics approaches 235 X. Conclusions and perspectives 235 Note added at the revision stage 236 Acknowledgements 236 References 236.

A proteoglycan mediates inductive interaction during plant vascular development

Inductive cell-cell interactions are essential for controlling cell fate determination in both plants and animals; however, the chemical basis of inductive signals in plants remains little understood. A proteoglycan-like factor named xylogen mediates local and inductive cell-cell interactions required for xylem differentiation in Zinnia cells cultured in vitro. Here we describe the purification of xylogen and cloning of its complementary DNA, and present evidence for its role in planta. The polypeptide backbone of xylogen is a hybrid-type molecule with properties of both arabinogalactan proteins and nonspecific lipid-transfer proteins. Xylogen predominantly accumulates in the meristem, procambium and xylem. In the xylem, xylogen has a polar localization in the cell walls of differentiating tracheary elements. Double knockouts of Arabidopsis lacking both genes that encode xylogen proteins show defects in vascular development: discontinuous veins, improperly interconnected vessel elements and simplified venation. Our results suggest that the polar secretion of xylogen draws neighbouring cells into the pathway of vascular differentiation to direct continuous vascular development, thereby identifying a molecule that mediates an inductive cell-cell interaction involved in plant tissue differentiation.

HD-Zip III Homeobox Genes that Include a Novel Member, ZeHB-13 (Zinnia)/ATHB-15 (Arabidopsis), are Involved in Procambium and Xylem Cell Differentiation

HD-Zip III homeobox genes are known to be essential transcriptional factors for vascular development. To further understand the relation of HD-Zip III genes in vascular differentiation, we isolated a new member of the HD-Zip III genes, ZeHB-13, as a Zinnia homolog of ATHB-15, and then characterized the expression profile using a Zinnia xylogenic cell culture and Zinnia plants. We compared the accumulation pattern of transcripts for ZeHB-13 and other HD-Zip III genes and suggested that the expression of ZeHB-13 was restricted to the procambium and was not severely suppressed by brassinazole, an inhibitor of brassinosteroid biosynthesis, unlike other HD-Zip III genes. We also characterized its Arabidopsis counterpart, ATHB-15. A histochemical promoter analysis using ATHB-15::GUS transgenic Arabidopsis plants indicated that ATHB-15 was active specifically in the procambium. These results strongly suggest that ZeHB-13/ATHB-15 is a pivotal transcriptional regulator responsible for early vascular development. Based on these results, we will discuss the regulation of xylem development in light of the functions of HD-Zip III members and brassinosteroids.

Transcriptional regulation of secondary growth in Arabidopsis thaliana

Despite its economic and environmental significance, understanding the molecular biology of secondary growth (i.e. wood formation) in tree species has been lagging behind that of primary growth, primarily due to the inherent difficulties of tree biology. In recent years, Arabidopsis has been shown to express all of the major components of secondary growth. Arabidopsis was induced to undergo secondary growth and the transcriptome profile changes were surveyed during secondary growth using 8.3 K Arabidopsis Genome Arrays. Twenty per cent of the approximately 8300 genes surveyed in this study were differentially regulated in the stems treated for wood formation. Genes of unknown function made up the largest category of the differentially expressed genes, followed by transcription regulation-related genes. Examination of the expression patterns of the genes involved in the sequential events of secondary growth (i.e. cell division, cell expansion, cell wall biosynthesis, lignification, and programmed cell death) identified several key candidate genes for the genetic regulation of secondary growth. In order to gain further insight into the transcriptional regulation of secondary growth, the expression patterns of the genes encoding transcription factors were documented in relation to secondary growth. A computational biology approach was used to identify regulatory cis-elements from the promoter regions of the genes that were up-regulated in wood-forming stems. The expression patterns of many previously unknown genes were established and various existing insights confirmed. The findings described in this report should add new information that can lead to a greater understanding of the secondary xylem formation process.

Preferential and asymmetrical accumulation of a Rac small GTPase mRNA in differentiating xylem cells of Zinnia elegans

Rac-type small GTPases are known to function in some cellular processes in plants. To further understand the involvement of Rac type GTPases in plant development, we isolated from cultured Zinnia cells a gene (ZeRAC2) encoding a new Rac-type small GTPase. ZeRAC2 mRNA accumulates preferentially in xylogenic culture and transiently at the time when visible tracheary elements appear. Experiments with ZeRAC2 recombinant proteins demonstrated that ZeRAC2 binds to and hydrolyzes GTP. A GFP-ZeRAC2 fusion protein was localized to the plasma membrane. Together with the fact that ZeRAC2 possesses a putative geranylgeranylation site at the C-terminus, this suggests that ZeRAC2 acts on the plasma membrane. In situ hybridization indicated that ZeRAC2 mRNA accumulates preferentially in xylem parenchyma and tracheary element precursor cells, and surprisingly the accumulation is restricted to the site facing developing tracheary elements.

Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells

Plants have a unique transdifferentiation mechanism by which differentiated cells can initiate a new program of differentiation. We used a comprehensive analysis of gene expression in an in vitro zinnia (Zinnia elegans L.) culture model system to gather fundamental information about the gene regulation underlying the transdifferentiation of plant cells. In this model, photosynthetic mesophyll cells isolated from zinnia leaves transdifferentiate into xylem cells in a morphogenic process characterized by features such as secondary-wall formation and programmed cell death. More than 8,000 zinnia cDNA clones were isolated from an equalized cDNA library prepared from cultured cells transdifferentiating into xylem cells. Microarray analysis using these cDNAs revealed several types of unique gene regulation patterns, including: the transient expression of a set of genes during cell isolation, presumably induced by wounding; a rapid reduction in the expression of photosynthetic genes and the rapid induction of protein synthesis-associated genes during the first stage; the preferential induction of auxin-related genes during the subsequent stage; and the transient induction of genes closely associated with particular morphogenetic events, including cell-wall formation and degradation and programmed cell death during the final stage. This analysis also revealed a number of previously uncharacterized genes encoding proteins that function in signal transduction, such as protein kinases and transcription factors that are expressed in a stage-specific manner. These findings provide new clues to the molecular mechanisms of both plant transdifferentiation and wood formation.

Phytochemicals in plants: genomics-assisted plant improvement for nutritional and health benefits

Plants are an important source of essential nutrients and health-beneficial components that are crucial for human life. Because the intake of these phytochemicals is not always adequate, the resources of plant biotechnology are being used to enhance the nutritional quality of our plant-based food supply. Various improvement strategies are feasible, depending on whether the phytochemical target is a major or minor constituent. Recent efforts in gene discovery and functional genomics are providing the necessary understanding to develop and evaluate different approaches to manipulate phytochemical composition.

Promotion of transcript accumulation of novel Zinnia immature xylem-specific HD-Zip III homeobox genes by brassinosteroids

We isolated three novel homeobox genes (ZeHB-10, -11 and -12) from Zinnia elegans to elucidate the molecular mechanism underlying vascular system formation. ZeHB-10, -11 and -12 encode for HD-Zip proteins of the class III to which Arabidopsis Athb-8, -9, -14, -15 and IFL1 belong. In situ hybridization analysis demonstrated that the ZeHB-10, -11 and -12 mRNAs accumulated preferentially in procambium and immature xylem cells in 14-day-old plants. Transcripts for the three genes also accumulated in cultured Zinnia cells in a xylogenesis-specific manner. The accumulation of transcripts for all of ZeHB-10, -11 and -12 in cultured Zinnia cells was suppressed strongly by uniconazole, an inhibitor of brassinosteroid synthesis, and such suppression was reversed by the addition of brassinolide, a biologically active brassinosteroid. Thus the expression of ZeHB-10, -11 and -12 may be regulated by endogenous levels of brassinosteroids. Taken together with the fact that ZeHB-10, -11 and -12 proteins can bind to each other in yeast, the roles of HD-Zip III genes in vascular development are discussed.

Enhancing mineral content in plant food products

Plant foods can serve as dietary sources of all essential minerals required by humans. Unfortunately, mineral concentrations are low in some plants, especially many staple food crops; thus, efforts are underway to increase the mineral content of these foods as a means to ensure adequate attainment of dietary minerals in all individuals. While these efforts have included classical breeding approaches in the past, it is clear that future progress can be made by utilizing the tools of biotechnology to effect directed changes in plant mineral status. Reviewed are the short- and long-distance mineral transport mechanisms responsible for the root acquisition and whole-plant partitioning of mineral ions in crop plants. This background is used to discuss different transgenic strategies with the potential to enhance mineral content in vegetative and/or reproductive tissues. Due to various constraints imposed by plant transport systems on whole-plant mineral movement, it is argued that modifications designed to increase the supply of minerals to edible organs should have the highest chance for success. Examples of previous efforts to manipulate plant mineral nutrition through the introduction of novel transgenes are presented to demonstrate the utility of these approaches.

Analysis of early processes in wound-induced vascular regeneration using TED3 and ZeHB3 as molecular markers

Interruption of the vascular bundles of Zinnia internodes induced transdifferentiation of cells into tracheary elements (TEs) or sieve elements (SEs) within 4 d of wounding. The early stage of the regeneration processes was analyzed using two molecular marker genes, TED3 and ZeHB3, which are expressed specifically in TE precursor cells and immature phloem cells, respectively. An increase in the numbers of TED3 and ZeHB3 mRNA-expressing cells always preceded an increase in the numbers of TEs and SEs formed. The earliest sign of vascular differentiation was the appearance 24 h after wounding of a layer(s) of TED3 mRNA-expressing cells in the inter- and intrafascicular cambial-like regions along the severed vascular bundles. In contrast, the number of ZeHB3 mRNA-expressing cells decreased dramatically along the severed bundles 24 h after wounding, and increased again 36 h after wounding. These results clearly indicate that xylem and phloem differentiation are not synchronized during vascular regeneration. Treatment with 10(-3) M colchicine abolished the expression of ZeHB3 mRNA in pith parenchyma, but not TED3 mRNA; this suggests that cell division is a prerequisite for the transdifferentiation of pith parenchymal cells into immature phloem cells expressing ZeHB3. In contrast, transdifferentiation of pith parenchymal cells to TE precursor cells does not require preceding cell division. However, the inhibition of cell division prevented the formation of both radial files of TEs and the cambial-like layer(s) of TED3 mRNA-expressing cells, and, ultimately, vascular regeneration altogether. These results imply that wound-induced cambial-like activity in and between severed vascular bundles is essential for vascular regeneration.