The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.

Asymmetric cell divisions play an important role in the establishment and propagation of the cellular pattern of plant tissues. The SHORT-ROOT (SHR) gene is required for the asymmetric cell division responsible for formation of ground tissue (endodermis and cortex) as well as specification of endodermis in the Arabidopsis root. We show that SHR encodes a putative transcription factor with homology to SCARECROW (SCR). From analyses of gene expression and cell identity in genetically stable and unstable alleles of shr, we conclude that SHR functions upstream of SCR and participates in a radial signaling pathway. Consistent with a regulatory role in radial patterning, ectopic expression of SHR results in supernumerary cell divisions and abnormal cell specification in the root meristem.

Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot.

Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. Analysis of the shoot phenotype of scr mutants revealed that both hypocotyl and shoot inflorescence also have a radial pattern defect, loss of a normal starch sheath layer, and consequently are unable to sense gravity in the shoot. Analogous to its expression in the endodermis of the root, SCR is expressed in the starch sheath of the hypocotyl and inflorescence stem. The SCR expression pattern in leaf bundle sheath cells and root quiescent center cells led to the identification of additional phenotypic defects in these tissues. SCR expression in a pin-formed mutant background suggested the possible origins of the starch sheath in the shoot inflorescence. Analysis of SCR expression and the mutant phenotype from the earliest stages of embryogenesis revealed a tight correlation between defective cell divisions and SCR expression in cells that contribute to ground tissue radial patterning in both embryonic root and shoot. Our data provides evidence that the same molecular mechanism regulates the radial patterning of ground tissue in both root and shoot during embryogenesis as well as postembryonically.

The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes.

Mutations at the SCARECROW (SCR) locus in Arabidopsis thaliana result in defective radial patterning in the root and shoot. The SCR gene product contains sequences which suggest that it is a transcription factor. A number of Arabidopsis Expressed Sequence Tags (ESTs) have been identified that encode gene products bearing remarkable similarity to SCR throughout their carboxyl-termini, indicating that SCR is the prototype of a novel gene family. These ESTs have been designated SCARECROW-LIKE (SCL). The gene products of the GIBBERELLIN-INSENSITIVE (GAI) and the REPRESSOR of ga1-3 (RGA) loci show high structural and sequence similarity to SCR and the SCLs. Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable amino-terminus and a highly conserved carboxyl-terminus that contains five recognizable motifs. The SCLs have distinct patterns of expression, but all of those analyzed show expression in the root. One of them, SCL3, has a tissue-specific pattern of expression in the root similar to SCR. The importance of the GRAS gene family in plant biology has been established by the functional analyses of SCR, GAI and RGA.

Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana.

Shoots of higher plants exhibit negative gravitropism. However, little is known about the mechanism or site of gravity perception in shoots. We have identified two loci that are essential for normal shoot gravitropism in Arabidopsis thaliana. Genetic analysis demonstrated that the shoot gravitropism mutants sgr1 and sgr7 are allelic to the radial pattern mutants, scr and shr, respectively. Characterization of the aerial phenotype of these mutants revealed that the primary defect is the absence of a normal endodermis in hypocotyls and influorescence stems. This indicates that the endodermis is essential for shoot gravitropism and strongly suggests that this cell layer functions as the gravity-sensing cell layer in dicotyledonous plant shoots. These results also demonstrate that, in addition to their previously characterized role in root radial patterning, SCR and SHR regulate the radial organization of the shoot axial organs in Arabidopsis.

Root development: signaling down and around.

Because of its elegant simplicity, the Arabidopsis root has become a model for studying plant organogenesis. In this review we focus on recent results indicating the importance of signaling in root development. A role for positional information in root cell specification has been demonstrated by ablation analyses. Through mutational analysis, genes have been identified that play a role in radial pattern formation. The embryonic phenotypes of these mutants raised the possibility that division patterns in post-embryonic roots are dependent on signaling that originates during embryonic development. Analysis of expression of the SCARECROW gene indicates that it may play a role in this 'top-down' signaling process. Characterization of root epidermis development has led to the identification of negative regulators of root-hair formation. These appear to set up a prepattern which is reinforced by signaling by plant hormones.

The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root.

In the Arabidopsis root meristem, initial cells undergo asymmetric divisions to generate the cell lineages of the root. The scarecrow mutation results in roots that are missing one cell layer owing to the disruption of an asymmetric division that normally generates cortex and endodermis. Tissue-specific markers indicate that a heterogeneous cell type is formed in the mutant. The deduced amino acid sequence of SCARECROW (SCR) suggests that it is a member of a novel family of putative transcription factors. SCR is expressed in the cortex/endodermal initial cells and in the endodermal cell lineage. Tissue-specific expression is regulated at the transcriptional level. These results indicate a key role for SCR in regulating the radial organization of the root.

A novel homeobox cluster expressed in repeated structures of the midgut.

A gene cluster (LOX3-C) containing three duplicated homeobox sequences (Lox3A, Lox3B, and Lox3C) was characterized in the leech Hirudo medicinalis. The leech homeoboxes have a limited homology to those of Antennapedia-class genes, but do not have homologs among currently characterized insect genes. The Lox3 genes belong to a new family, named Xlox, that also includes genes from mouse, rat, frog, and a distantly related leech, Helobdella triserialis. All members of the Xlox family are expressed in specific regions of the embryonic gut, where they seem to affect morphogenesis and cell differentiation. The three homeoboxes of LOX3-C described here are contained within nearly identical direct tandem repeats. The LOX3-C region produces at least two transcripts, one present in both embryos and adults and the other only in early embryos. Early Lox3 expression is restricted to specific regions of the midgut primordium, in 12 segmentally repeated, transverse stripes of fusiform cells found at the positions where the midgut will constrict to form the 11 diverticula of the crop. A role in the development of segmentally iterated structures in an initially homogeneous midgut is proposed for LOX3-C.

Antennapedia-class homebox genes define diverse neuronal sets in the embryonic CNS of the leech.

Studies of the Antennapedia-class homeobox genes suggest that specific combinations of these transcription factors play a role in defining neuronal identities. We examined the expression of these genes in the leech Hirudo medicinalis, an organism well-suited for neurobiological research at the level of identified neurons. Leeches contain at least as many Antennapedia-class and related genes as insects do, despite the apparently lower complexity of the leech body plan. The CNS expression patterns of two Antennapedia-class leech homeobox genes (Lox genes) were examined in detail. Lox1 is expressed during early gangliogenesis in only one pair of transient neurons present in every segment (the Bipolar cells) and, at later stages of embryonic development, in 15-20 pairs of central neurons repeated in most segments. The monoclonal antibody Laz1-1 identified two pairs of Lox1-expressing neurons as the Bipolar cells and the L1 neurons. The Bipolar cells extended processes in the primordia of the longitudinal connective nerves and later degenerated. The L1 neurons were detected late in gangliogenesis and became stable neurons. Lox2 is expressed in an iterated set of neurons in the posterior two-thirds of the CNS. On the basis of cell body position and relative size, two pairs of Lox2-expressing cells were identified as the RPE-like neurons and the CV motor neurons. Other Lox genes are also expressed in segmentally repeated subpopulations of neurons. These neuronal subpopulations appear to be different from one another but partially overlapping. Different combinations of Lox genes that may be expressed in individual cells could in theory generate enough variability to specify all central neurons in a leech ganglion.

Characterization of a homologue of bithorax-complex genes in the leech Hirudo medicinalis.

We report the isolation and characterization of the Hirudo medicinalis homoeobox gene Lox2. Sequence analysis shows that it contains a region that has homology to Drosophila and vertebrate homoeodomains of the Antennapedia class. In addition, Lox2 shares homology with sequences in the bithorax complex Ultra-bithorax (Ubx) and abdominal A (abdA) genes in a region adjacent to the C-terminus of the homoeodomain. Whole mount in situ hybridization of embryos of various ages demonstrates that during early development this gene has temporally and spatially restricted patterns of expression that resemble those of the homoeotic genes of the Drosophila bithorax complex and of many vertebrate homoeobox genes. The largest accumulation of transcripts was seen in the posterior two-thirds of the developing leech central nervous system in 7-14-day-old embryos. Adult leeches also express Lox2. We propose that in Hirudo, Lox2 represents the ancestral gene of the Ubx and abdA genes of the bithorax complex of Drosophila.