The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

Arabidopsis Landsberg erecta is one of the most popular ecotypes and is used widely for both molecular and genetic studies. It harbors the erecta (er) mutation, which confers a compact inflorescence, blunt fruits, and short petioles. We have identified five er mutant alleles from ecotypes Columbia and Wassilewskija. Phenotypic characterization of the mutant alleles suggests a role for the ER gene in regulating the shape of organs originating from the shoot apical meristem. We cloned the ER gene, and here, we report that it encodes a putative receptor protein kinases. The deduced ER protein contains a cytoplasmic protein kinase catalytic domain, a transmembrane region, and an extracellular domain consisting of leucine-rich repeats, which are thought to interact with other macromolecules. Our results suggest that cell-cell communication mediated by a receptor kinase has an important role in plant morphogenesis.

The Arabidopsis thaliana genome sequencing project has revealed that multigene families, such as those generated by genome duplications, are more abundant among plant genomes than among animal genomes. To gain insight into the evolutionary implications of the multigene families in higher plants, we examined the XTH gene family, a group of genes encoding xyloglucan endotransglucosylase/hydrolase, which are responsible for cell-wall construction in plants. Expression analysis of all members (33 genes) of this family, using quantitative real-time RT-PCR, revealed that most members exhibit distinct expression profiles in terms of tissue specificity and responses to hormonal signals, with some members exhibiting similar expression patterns. By comparing the flanking sequences of individual genes, we identified four sets of large-segment duplications and two sets of solitary gene duplications. In each set of gene duplicates, long nucleotide sequences, ranging from one to two hundred base pairs, are conserved. Furthermore, gene duplicates exhibit similar organ-specific expression profiles. These facts allowed us to predict putative cis-regulatory regions, particularly those responsible for cell-wall construction, and hence for morphogenesis, that are specific for certain organs or tissues in plants.

Arabidopsis Landsberg erecta is one of the most popular ecotypes and is used widely for both molecular and genetic studies. It harbors the erecta (er) mutation, which confers a compact inflorescence, blunt fruits, and short petioles. We have identified five er mutant alleles from ecotypes Columbia and Wassilewskija. Phenotypic characterization of the mutant alleles suggests a role for the ER gene in regulating the shape of organs orlginating f" the shoot apical meristem. We cloned the ER gene, and here, we report that it encades a putative receptor protein klnase. The deduced ER protein contains a cytoplasmic protein kinase catalytic domain, a transmembrane region, and an extracellular domain consisting of leucine-rich repeats, which are thought to interact with other macromolecules. Our results suggest that cell-cell communication mediated by a receptor kinase has an important role in plant morphogenesis.

We previously showed that the ANGUSTIFOLIA (AN) gene regulates the width of leaves of Arabidopsis thaliana, by controlling the polar elongation of leaf cells. In the present study, we found that the abnormal arrangement of cortical microtubules (MTs) in an leaf cells appeared to account entirely for the abnormal shape of the cells. It suggested that the AN gene might regulate the polarity of cell growth by controlling the arrangement of cortical MTs. We cloned the AN gene using a map-based strategy and identified it as the first member of the CtBP family to be found in plants. Wild-type AN cDNA reversed the narrow-leaved phenotype and the abnormal arrangement of cortical MTs of the an-1 mutation. In the animal kingdom, CtBPs self-associate and act as co-repressors of transcription. The AN protein can also self-associate in the yeast two-hybrid system. Furthermore, microarray analysis suggested that the AN gene might regulate the expression of certain genes, e.g. the gene involved in formation of cell walls, MERI5. A discussion of the molecular mechanisms involved in the leaf shape regulation is presented based on our observations.

A search of the recently completed genomic database of rice (Oryza sativa) identified a 29-member xyloglucan endotransglucosylase/hydrolase (OsXTH) gene family. This first report of a complete XTH family from a monocotyledonous species reveals that the OsXTH family is comparable in size with that of the dicotyledon Arabidopsis thaliana, which consists of 33 AtXTH genes. This is surprising because xyloglucan, the specific substrate of XTHs, is considerably less abundant in cell walls of monocotyledons than dicotyledons and is not typically ascribed an important structural role in monocotyledons. As a first step toward determining the roles of rice XTHs, the expression patterns of all 29 OsXTH genes were examined using a quantitative DNA microarray procedure with gene-specific oligonucleotide probes. The analysis showed that most members of the rice XTH family exhibited organ-and growth stage-specific expression. This was confirmed by quantitative real-time reverse transcriptase-polymerase chain reaction analysis of representative OsXTH members. This revealed in more detail the temporally and spatially controlled expression profiles of individual OsXTH genes at particular sites in rice. Previous reports indicated that grasses have relatively greater xyloglucan endotransglucosylase activities, one of the two enzyme activities catalyzed by XTHs, than in equivalent tissues in dicotyledons. This observation, together with the tissue-specific and growth stage-dependent expression of a large rice XTH gene family, suggests that xyloglucan metabolism plays a more central role in monocotyledon cell wall restructuring than has been reported previously.The most widely adopted models of the structure of primary cell walls in dicotyledonous plants view the hemicellulose xyloglucan as a structurally important glycan (Carpita and Gibeaut, 1993), cross-linking and tethering cellulose microfibrils, and thereby forming the basic load-bearing framework of these so-called type I walls (Carpita, 1996). Other models place less emphasis on xyloglucan cross-links but still envisage xyloglucan as interacting closely with the microfibrils (for review, see Cosgrove, 2000). Xyloglucans are found in type I cell walls in various tissues at different developmental stages, including the cell plates formed in dividing cells (Moore and Staehelin, 1988), the primary walls in growing cell, and fully differentiated secondary walls. Given its proposed important structural role, there is considerable interest in understanding the biochemical basis of xyloglucan synthesis, integration into the wall and subsequent modification: all processes that are considered to be a fundamental part of cell growth and differentiation.The xyloglucan endotransglucosylase/hydrolases (XTHs) are a family of enzymes that specifically use xyloglucan as a substrate and that catalyze xyloglucan endotransglucosylase (XET) and/or xyloglucan endohydrolase activities. Thus, XTHs are thought to play an important role in the construction and restructuring of xyloglucan cross-links,...

Most plants do poorly when flooded. Certain rice varieties, known as deepwater rice, survive periodic flooding and consequent oxygen deficiency by activating internode growth of stems to keep above the water. Here, we identify the gibberellin biosynthesis gene, (), whose loss-of-function allele catapulted the rice Green Revolution, as being responsible for submergence-induced internode elongation. When submerged, plants carrying the deepwater rice-specific haplotype amplify a signaling relay in which the gene is transcriptionally activated by an ethylene-responsive transcription factor, OsEIL1a. The SD1 protein directs increased synthesis of gibberellins, largely GA, which promote internode elongation. Evolutionary analysis shows that the deepwater rice-specific haplotype was derived from standing variation in wild rice and selected for deepwater rice cultivation in Bangladesh.

Some plants can avoid shaded conditions via rapid shoot elongation, thus growing into better lit areas in a canopy. Cell wallmodifying mechanisms promoting this elongation response, therefore, are important regulatory points during shade avoidance. Two major cell wall-modifying protein families are expansins and xyloglucan endotransglucosylase/hydrolases (XTHs). The role of these proteins during shade avoidance was studied in Arabidopsis (Arabidopsis thaliana). In response to two shade cues, low red to far-red light (implying neighbor proximity) and green shade (mimicking dense canopy conditions), Arabidopsis showed classic shade avoidance features: petiole elongation and leaf hyponasty. Measurement of the apoplastic proton flux in green shade-treated petioles revealed a rapid efflux of protons into the apoplast within minutes, unlike white light controls. This apoplastic acidification probably provides the acidic pH required for the optimal activity of cell wallmodifying proteins like expansins and XTHs. Acid-induced extension, expansin susceptibility, and extractable expansin activity were similar in petioles from white light-and shade-treated plants. XTH activity, however, was high in petioles exposed to shade treatments. Five XTH genes (XTH9, were positively regulated by low red to far-red light conditions, while the latter four and XTH22 showed a significant up-regulation also in response to green shade. Consistently, knockout mutants for two of these XTH genes also had reduced or absent shade avoidance responses to these light signals. These results point toward the cell wall as a vital regulatory point during shade avoidance.