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Philip N Benfey

Publications and source records attributed to Philip N Benfey.

At least 19 recordsLinked to original sources
PubMed2006

Combining expression and comparative evolutionary analysis. The COBRA gene family.

Plant cell shape is achieved through a combination of oriented cell division and cell expansion and is defined by the cell wall. One of the genes identified to influence cell expansion in the Arabidopsis (Arabidopsis thaliana) root is the COBRA (COB) gene that belongs to a multigene family. Three members of the AtCOB gene family have been shown to play a role in specific types of cell expansion or cell wall biosynthesis. Functional orthologs of one of these genes have been identified in maize (Zea mays) and rice (Oryza sativa; Schindelman et al., 2001; Li et al., 2003; Brown et al., 2005; Persson et al., 2005; Ching et al., 2006; Jones et al., 2006). We present the maize counterpart of the COB gene family and the COB gene superfamily phylogeny. Most of the genes belong to a family with two main clades as previously identified by analysis of the Arabidopsis family alone. Within these clades, however, clear differences between monocot and eudicot family members exist, and these are analyzed in the context of Type I and Type II cell walls in eudicots and monocots. In addition to changes at the sequence level, gene regulation of this family in a eudicot, Arabidopsis, and a monocot, maize, is also characterized. Gene expression is analyzed in a multivariate approach, using data from a number of sources, including massively parallel signature sequencing libraries, transcriptional reporter fusions, and microarray data. This analysis has revealed that the expression of Arabidopsis and maize COB gene family members is highly developmentally and spatially regulated at the tissue and cell type-specific level, that gene superfamily members show overlapping and unique expression patterns, and that only a subset of gene superfamily members act in response to environmental stimuli. Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB.

Amino Acid Sequence↗
PubMed2006

Transcription factors and hormones: new insights into plant cell differentiation.

Plant development is a continuous process, mainly due to the presence of stem cell niches within the root and shoot. The interplay between a host of transcription factors determines whether the cells within the meristem maintain their stem cell state, differentiate into leaves or form secondary meristems, which develop into shoots and flowers. Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation.

Cell Differentiation↗
PubMed2006

Quantification of transcription factor expression from Arabidopsis images.

MOTIVATION: Confocal microscopy has long provided qualitative information for a variety of applications in molecular biology. Recent advances have led to extensive image datasets, which can now serve as new data sources to obtain quantitative gene expression information. In contrast to microarrays, which usually provide data for many genes at one time point, these image data provide us with expression information for only one gene, but with the advantage of high spatial and/or temporal resolution, which is often lostin microarray samples. RESULTS: We have developed a prototype for the automatic analysis of Arabidopsis confocal images, which show the expression of a single transcription factor by means of GFP reporter constructs. Using techniques from image registration, we are able to address inherent problems of non-rigid transformation and partial mapping, and obtain relative expression values for 13 different tissues in Arabidopsis roots. This provides quantitative information with high spatial resolution, which accurately represents the underlying expression values within the organism. We validate our approach on a data set of 122 images depicting expression patterns of 30 transcription factors, both in terms of registration accuracy, as well as correlation with cell-sorted microarray data. Approaches like this will be useful to lay the groundwork to reconstruct regulatory networks on the level of tissues or even individual cells. AVAILABILITY: Upon request from the authors.

Arabidopsis Proteins↗
PubMed2006

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.

Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway.

Arabidopsis↗
PubMed2006

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.

Understanding how the expression of transcription factor (TF) genes is modulated is essential for reconstructing gene regulatory networks. There is increasing evidence that sequences other than upstream noncoding can contribute to modulating gene expression, but how frequently they do so remains unclear. Here, we investigated the regulation of TFs expressed in a tissue-enriched manner in Arabidopsis roots. For 61 TFs, we created GFP reporter constructs driven by each TF's upstream noncoding sequence (including the 5'UTR) fused to the GFP reporter gene alone or together with the TF's coding sequence. We compared the visually detectable GFP patterns with endogenous mRNA expression patterns, as defined by a genome-wide microarray root expression map. An automated image analysis method for quantifying GFP signals in different tissues was developed and used to validate our visual comparison method. From these combined analyses, we found that (i) the upstream noncoding sequence was sufficient to recapitulate the mRNA expression pattern for 80% (35/44) of the TFs, and (ii) 25% of the TFs undergo posttranscriptional regulation via microRNA-mediated mRNA degradation (2/24) or via intercellular protein movement (6/24). The results suggest that, for Arabidopsis TFs, upstream noncoding sequences are major contributors to mRNA expression pattern establishment, but modulation of transcription factor protein expression pattern after transcription is relatively frequent. This study provides a systematic overview of regulation of TF expression at a cellular level.

Arabidopsis↗
PubMed2005

Transcriptional profile of the Arabidopsis root quiescent center.

The self-renewal characteristics of stem cells render them vital engines of development. To better understand the molecular mechanisms that determine the properties of stem cells, transcript profiling was conducted on quiescent center (QC) cells from the Arabidopsis thaliana root meristem. The AGAMOUS-LIKE 42 (AGL42) gene, which encodes a MADS box transcription factor whose expression is enriched in the QC, was used to mark these cells. RNA was isolated from sorted cells, labeled, and hybridized to Affymetrix microarrays. Comparisons with digital in situ expression profiles of surrounding tissues identified a set of genes enriched in the QC. Promoter regions from a subset of transcription factors identified as enriched in the QC conferred expression in the QC. These studies demonstrated that it is possible to successfully isolate and profile a rare cell type in the plant. Mutations in all enriched transcription factor genes including AGL42 exhibited no detectable root phenotype, raising the possibility of a high degree of functional redundancy in the QC.

Arabidopsis↗
PubMed2005

COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation.

The orientation of cell expansion is a process at the heart of plant morphogenesis. Cellulose microfibrils are the primary anisotropic material in the cell wall and thus are likely to be the main determinant of the orientation of cell expansion. COBRA (COB) has been identified previously as a potential regulator of cellulose biogenesis. In this study, characterization of a null allele, cob-4, establishes the key role of COB in controlling anisotropic expansion in most developing organs. Quantitative polarized-light and field-emission scanning electron microscopy reveal that loss of anisotropic expansion in cob mutants is accompanied by disorganization of the orientation of cellulose microfibrils and subsequent reduction of crystalline cellulose. Analyses of the conditional cob-1 allele suggested that COB is primarily implicated in microfibril deposition during rapid elongation. Immunodetection analysis in elongating root cells revealed that, in agreement with its substitution by a glycosylphosphatidylinositol anchor, COB was polarly targeted to both the plasma membrane and the longitudinal cell walls and was distributed in a banding pattern perpendicular to the longitudinal axis via a microtubule-dependent mechanism. Our observations suggest that COB, through its involvement in cellulose microfibril orientation, is an essential factor in highly anisotropic expansion during plant morphogenesis.

Arabidopsis↗
PubMed2005

Not just another hole in the wall: understanding intercellular protein trafficking.

Development and differentiation of multicellular organisms requires cell-to-cell communication. In plants direct signaling and exchange of macromolecules between cells is possible through plasmodesmata. Recently direct exchange of membrane-bound vesicles and organelles has been demonstrated between animal cells through formation of cytoplasmic bridges (tunneling nanotubes) in vitro. Here we review recent developments in cell-to-cell trafficking of macromolecules in plants and animals.

Animals↗
PubMed2005

Conservation and diversification of SCARECROW in maize.

The SCARECROW (SCR) gene in Arabidopsis is required for asymmetric cell divisions responsible for ground tissue formation in the root and shoot. Previously, we reported that Zea mays SCARECROW (ZmSCR) is the likely maize ortholog of SCR. Here we describe conserved and divergent aspects of ZmSCR. Its ability to complement the Arabidopsis scr mutant phenotype suggests conservation of function, yet its expression pattern during embryogenesis and in the shoot system indicates divergence. ZmSCR expression was detected early during embryogenesis and localized to the endodermal lineage in the root, showing a gradual regionalization of expression. Expression of ZmSCR appeared to be analogous to that of SCR during leaf formation. However, its absence from the maize shoot meristem and its early expression pattern during embryogenesis suggest a diversification of ZmSCR in the patterning processes in maize. To further investigate the evolutionary relationship of SCR and ZmSCR, we performed a phylogenetic analysis using Arabidopsis, rice and maize SCARECROW-LIKE genes (SCLs). We found SCL23 to be the most closely related to SCR in both eudicots and monocots, suggesting that a gene duplication resulting in SCR and SCL23 predates the divergence of dicots and monocots.

Arabidopsis↗
PubMed2005

Signals that regulate stem cell activity during plant development.

Plant stem cells are used continuously to generate new structures during the entire life-span of the organism. In the adult plant, stem cells are found in specialized structures called meristems. The meristems contain the stem cell niche together with rapidly dividing daughter cells that will ultimately differentiate into specific cell types. Some of the master genes that orchestrate the establishment and maintenance of the stem cell niche have now been identified in both the root and the shoot. Recent results show that these genes also determine the fate of the stem cells and that feedback signals from differentiated cells are involved in stem cell specification. These advances have provided a framework to understand how short-range and long-range signals are integrated to specify and position the stem cell niche in the meristems, and how the differentiation potential of plant stem cells is controlled.

Cell Differentiation↗
PubMed2004

Mechanisms regulating SHORT-ROOT intercellular movement.

Signaling centers within developing organs regulate morphogenesis in both plants and animals. The putative transcription factor SHORT-ROOT (SHR) is an organizing signal regulating the division of specific stem cells in the Arabidopsis root. Comparison of gene transcription with protein localization indicates that SHR moves in a highly specific manner from the cells of the stele in which it is synthesized outward. Here, we provide evidence that SHR intercellular trafficking is both regulated and targeted. First, we show that subcellular localization of SHR in the stele is intrinsic to the SHR protein. Next, we show that SHR must be present in the cytoplasm to move, providing evidence that SHR movement is regulated. Finally, we describe an informative new shr allele, in which the protein is present in the cytoplasm yet does not move. Thus, in contrast to proteins that move by a process resembling diffusion, a cytoplasmic pool of SHR is not sufficient for movement.

Arabidopsis↗