Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants.

Arbuscular mycorrhizal fungi (AMF) can help mitigate plant responses to water stress, but it is unclear whether AMF do so by indirect mechanisms, direct water transport to roots, or a combination of the two. Here, we investigated if and how the AMF Rhizophagus intraradices transported water to the host plant Avena barbata, wild oat. We used two-compartment microcosms, isotopically labeled water, and a fluorescent dye to directly track and quantify water transport by AMF across an air gap to host plants. Plants grown with AMF that had access to a physically separated compartment containing 18 O-labeled water transpired almost twice as much as plants with AMF excluded from that compartment. Using an isotopic mixing model, we estimated that water transported by AMF across the air gap accounted for 34.6% of the water transpired by host plants. In addition, a fluorescent dye indicated that hyphae were able to transport some water via an extracytoplasmic pathway. Our study provides direct evidence that AMF can act as extensions of the root system along the soil-plant-air continuum of water movement, with plant transpiration driving water flow along hyphae outside of the hyphal cell membrane.

Longitudinal patterning in roots: a GATA2-auxin interaction underlies and maintains the root transition domain.

MAIN CONCLUSION: In Arabidopsis thaliana root meristems the GATA2 transcription factor is a marker for the root transition domain, is auxin regulated, and functions to restrict cell division activity. The growing part of roots is comprised of three discrete regions; the proliferative domain (PD), an elongation zone, and interposed between these two, the transition domain (TD), which is the focus of this investigation. Within the TD, it is hypothesized that cells are reprogrammed, losing the capacity to divide and begin to differentiate. In recently germinated Arabidopsis thaliana seedlings, a TD is not anatomically evident, but subsequently forms in a region of the root in which there has occurred prior expression of both AUX1/PIN2 proteins and of transcripts of the GATA transcription factor family (pGATA2:H2B-YFP or pGATA2:GUS). pGATA2:GUS expression is regulated by auxin and is reduced in seedlings in which either auxin transport or auxin sensitivity is perturbed. Application of cytokinin results in a reduction in both pGATA2:GUS expression and in TD cell number, via a pathway involving ARR1 and ARR12. Overexpression of GATA2 is accompanied by a reduction in cell number in the PD, but has no effect on cell number in the TD, whereas in knockdowns of GATA transcription factors, cell number is reduced in both the PD and TD. We conclude: (1) that GATA2 expression is localized to (a marker for) the TD; (2) that development and maintenance of the TD are associated with an auxin-regulation of GATA2 expression; (3) that GATA transcription factors function to restrict cell division activity.

CLE-like (CLEL) peptides control the pattern of root growth and lateral root development in Arabidopsis.

CLE peptides, named for the CLV3/ESR-related peptide family, participate in intercellular-signaling pathways. Here we investigated members of the CLE-like (CLEL) gene family that encode peptide precursors recently designated as root growth factors [Matsuzaki Y et al. (2010) Science 329:1065-1067]. CLEL precursors share a similar domain structure with CLE precursors (i.e., they contain a putative N-terminal signal peptide and a C-terminal conserved 13-amino-acid CLEL motif with a variable middle portion). Our evidence shows that, unlike root growth factor, CLEL peptides are (i) unmodified and (ii) function in the regulation of the direction of root growth and lateral root development. Overexpression of several CLEL genes in Arabidopsis resulted in either long roots or long and wavy roots that also showed altered lateral root patterning. Exogenous application of unmodified synthetic 13-amino-acid peptides derived from two CLEL motifs resulted in similar phenotypic changes in roots of wild-type plants. In CLEL peptide-induced long roots, the root apical meristem (RAM) was enlarged and consisted of an increased number of cells, compared with wild-type root apical meristems. The wavy-root phenotype appeared to be independent of other responses of the roots to the environment (e.g., gravitropism, phototropism, and thigmotropism). Results also showed that the inhibition of lateral initiation by CLEL overexpression was not overcome by the application of auxin. These findings establish CLEL as a peptide family with previously unrecognized regulatory functions controlling the pattern of root growth and lateral root development in plants.

Using biologically interrelated experiments to identify pathway genes in Arabidopsis.

MOTIVATION: Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing genes in pathways remain challenging. RESULTS: In this work, we elucidate higher level gene-gene interactions by evaluating the conditional dependencies between genes, i.e. the relationships between genes after removing the influences of a set of previously known pathway genes. These previously known pathway genes serve as seed genes in our model and will guide the detection of other genes involved in the same pathway. The detailed statistical techniques involve the estimation of a precision matrix whose elements are known to be proportional to partial correlations (i.e. conditional dependencies) between genes under appropriate normality assumptions. Likelihood ratio tests on two forms of precision matrices are further performed to see if a candidate pathway gene is conditionally independent of all the previously known pathway genes. When used effectively, this is a promising approach to recover gene relationships that would have otherwise been missed by standard methods. The advantage of the proposed method is demonstrated using both simulation studies and real datasets. We also demonstrated the importance of taking into account experimental dependencies in the simulation and real data studies.

A membrane-associated thioredoxin required for plant growth moves from cell to cell, suggestive of a role in intercellular communication.

Thioredoxins (Trxs) are small ubiquitous regulatory disulfide proteins. Plants have an unusually complex complement of Trxs composed of six well-defined types (Trxs f, m, x, y, h, and o) that reside in different cell compartments and function in an array of processes. The extraplastidic h type consists of multiple members that in general have resisted isolation of a specific phenotype. In analyzing mutant lines in Arabidopsis thaliana, we identified a phenotype of dwarf plants with short roots and small yellowish leaves for AtTrx h9 (henceforth, Trx h9), a member of the Arabidopsis Trx h family. Trx h9 was found to be associated with the plasma membrane and to move from cell to cell. Controls conducted in conjunction with the localization of Trx h9 uncovered another h-type Trx in mitochondria (Trx h2) and a Trx in plastids earlier described as a cytosolic form in tomato. Analysis of Trx h9 revealed a 17-amino acid N-terminal extension in which the second Gly (Gly(2)) and fourth cysteine (Cys(4)) were highly conserved. Mutagenesis experiments demonstrated that Gly(2) was required for membrane binding, possibly via myristoylation. Both Gly(2) and Cys(4) were needed for movement, the latter seemingly for protein structure and palmitoylation. A three-dimensional model was consistent with these predictions as well as with earlier evidence showing that a poplar ortholog is reduced by a glutaredoxin rather than NADP-thioredoxin reductase. In demonstrating the membrane location and intercellular mobility of Trx h9, the present results extend the known boundaries of Trx and suggest a role in cell-to-cell communication.

Principal growth directions in development of the lateral root in Arabidopsis thaliana.

BACKGROUND AND AIMS: During lateral root development a new meristem is formed within the mother root body. The main objective of this work was to simulate lateral root formation in Arabidopsis thaliana and to study a potential role of the principal directions in this process. Lateral root growth is anisotropic, so that three principal directions of growth can be distinguished within the organ. This suggests a tensorial character of growth and allows for its description by means of the growth tensor method. METHODS: First features of the cell pattern of developing lateral roots were analysed in A. thaliana and then a tensorial model for growth and division of cells for this case was specified, assuming an unsteady character of the growth field of the organ. KEY RESULTS: Microscopic observations provide evidence that the principal directions of growth are manifested at various developmental stages by oblique cell walls observed in different regions of the primordium. Other significant features observed are atypically shaped large cells at the flanks of young apices, as well as distinct boundaries between the mother root and the primordium. Simulations were performed using a model for growth. In computer-generated sequences the above-mentioned features could be identified. An attempt was made to reconstruct the virtual lateral root that included a consideration of the formation of particular tissue types based on literature data. CONCLUSIONS: In the cell pattern of the developing lateral root the principal directions of growth can be recognized through occurrence of oblique cell divisions. In simulation the role of these directions in cell pattern formation was confirmed, only when cells divide with respect to the principal directions can realistic results be obtained.

Comprehensive analysis of CLE polypeptide signaling gene expression and overexpression activity in Arabidopsis.

Intercellular signaling is essential for the coordination of growth and development in higher plants. Although hundreds of putative receptors have been identified in Arabidopsis (Arabidopsis thaliana), only a few families of extracellular signaling molecules have been discovered, and their biological roles are largely unknown. To expand our insight into the developmental processes potentially regulated by ligand-mediated signal transduction pathways, we undertook a systematic expression analysis of the members of the Arabidopsis CLAVATA3/ESR-RELATED (CLE) small signaling polypeptide family. Using reporter constructs, we show that the CLE genes have distinct and specific patterns of promoter activity. We find that each Arabidopsis tissue expresses at least one CLE gene, indicating that CLE-mediated signaling pathways are likely to play roles in many biological processes during the plant life cycle. Some CLE genes that are closely related in sequence have dissimilar expression profiles, yet in many tissues multiple CLE genes have overlapping patterns of promoter-driven reporter activity. This observation, plus the general absence of detectable morphological phenotypes in cle null mutants, suggest that a high degree of functional redundancy exists among CLE gene family members. Our work establishes a community resource of CLE-related biological materials and provides a platform for understanding and ultimately manipulating many different plant signaling systems.

CLE14/CLE20 peptides may interact with CLAVATA2/CORYNE receptor-like kinases to irreversibly inhibit cell division in the root meristem of Arabidopsis.

Towards an understanding of the interacting nature of the CLAVATA (CLV) complex, we predicted the 3D structures of CLV3/ESR-related (CLE) peptides and the ectodomain of their potential receptor proteins/kinases, and docking models of these molecules. The results show that the ectodomain of CLV1 can form homodimers and that the 12-/13-amino-acid CLV3 peptide fits into the binding clefts of the CLV1 dimers. Our results also demonstrate that the receptor domain of CORYNE (CRN), a recently identified receptor-like kinase, binds tightly to the ectodomain of CLV2, and this likely leads to an increased possibility for docking with CLV1. Furthermore, our docking models reveal that two CRN-CLV2 ectodomain heterodimers are able to form a tetramer receptor complex. Peptides of CLV3, CLE14, CLE19, and CLE20 are also able to bind a potential CLV2-CRN heterodimer or heterotetramer complex. Using a cell-division reporter line, we found that synthetic 12-amino-acid CLE14 and CLE20 peptides inhibit, irreversibly, root growth by reducing cell division rates in the root apical meristem, resulting in a short-root phenotype. Intriguingly, we observed that exogenous application of cytokinin can partially rescue the short-root phenotype induced by over-expression of either CLE14 or CLE20 in planta. However, cytokinin treatment does not rescue the short-root phenotype caused by exogenous application of the synthetic CLE14/CLE20 peptides, suggesting a requirement for a condition provided only in living plants. These results therefore imply that the CLE14/CLE20 peptides may act through the CLV2-CRN receptor kinase, and that their availabilities and/or abundances may be affected by cytokinin activity in planta.

The maize root stem cell niche: a partnership between two sister cell populations.

Using transcript profile analysis, we explored the nature of the stem cell niche in roots of maize (Zea mays). Toward assessing a role for specific genes in the establishment and maintenance of the niche, we perturbed the niche and simultaneously monitored the spatial expression patterns of genes hypothesized as essential. Our results allow us to quantify and localize gene activities to specific portions of the niche: to the quiescent center (QC) or the proximal meristem (PM), or to both. The data point to molecular, biochemical and physiological processes associated with the specification and maintenance of the niche, and include reduced expression of metabolism-, redox- and certain cell cycle-associated transcripts in the QC, enrichment of auxin-associated transcripts within the entire niche, controls for the state of differentiation of QC cells, a role for cytokinins specifically in the PM portion of the niche, processes (repair machinery) for maintaining DNA integrity and a role for gene silencing in niche stabilization. To provide additional support for the hypothesized roles of the above-mentioned and other transcripts in niche specification, we overexpressed, in Arabidopsis, homologs of representative genes (eight) identified as highly enriched or reduced in the maize root QC. We conclude that the coordinated changes in expression of auxin-, redox-, cell cycle- and metabolism-associated genes suggest the linkage of gene networks at the level of transcription, thereby providing additional insights into events likely associated with root stem cell niche establishment and maintenance.

Measuring similarities between gene expression profiles through new data transformations.

BACKGROUND: Clustering methods are widely used on gene expression data to categorize genes with similar expression profiles. Finding an appropriate (dis)similarity measure is critical to the analysis. In our study, we developed a new measure for clustering the genes when the key factor is the shape of the profile, and when the expression magnitude should also be accounted for in determining the gene relationship. This is achieved by modeling the shape and magnitude parameters separately in a gene expression profile, and then using the estimated shape and magnitude parameters to define a measure in a new feature space. RESULTS: We explored several different transformation schemes to construct the feature spaces that include a space whose features are determined by the mutual differences of the original expression components, a space derived from a parametric covariance matrix, and the principal component space in traditional PCA analysis. The former two are the newly proposed and the latter is explored for comparison purposes. The new measures we defined in these feature spaces were employed in a K-means clustering procedure to perform analyses. Applying these algorithms to a simulation dataset, a developing mouse retina SAGE dataset, a small yeast sporulation cDNA dataset, and a maize root affymetrix microarray dataset, we found from the results that the algorithm associated with the first feature space, named TransChisq, showed clear advantages over other methods. CONCLUSION: The proposed TransChisq is very promising in capturing meaningful gene expression clusters. This study also demonstrates the importance of data transformations in defining an efficient distance measure. Our method should provide new insights in analyzing gene expression data. The clustering algorithms are available upon request.

Salt Stress Affects the Redox Status of Arabidopsis Root Meristems.

We report the redox status (profiles) for specific populations of cells that comprise the Arabidopsis root tip. For recently germinated, 3-5-day-old seedlings we show that the region of the root tip with the most reduced redox status includes the root cap initials, the quiescent center and the most distal portion of the proximal meristem, and coincides with (overlays) the region of the auxin maximum. As one moves basally, further into the proximal meristem, and depending on the growth conditions, the redox status becomes more oxidized, with a 5-10 mV difference in redox potential between the two borders delimiting the proximal meristem. At the point on the root axis at which cells of the proximal meristem cease division and enter the transition zone, the redox potential levels off, and remains more or less unchanged throughout the transition zone. As cells leave the transition zone and enter the zone of elongation the redox potentials become more oxidized. Treating roots with salt (50, 100, and 150 mM NaCl) results in marked changes in root meristem structure and development, and is preceded by changes in the redox profile, which flattens, and initially becomes more oxidized, with pronounced changes in the redox potentials of the root cap, the root cap initials and the quiescent center. Roots exposed to relatively mild levels of salt (<100 mM) are able to re-establish a normal, pre-salt treatment redox profile 3-6 days after exposure to salt. Coincident with the salt-associated changes in redox profiles are changes in the distribution of auxin transporters (AUX1, PIN1/2), which become more diffuse in their localization. We conclude that salt stress affects root meristem maintenance, in part, through changes in redox and auxin transport.

Assessing the regulation of leaf redox status under water stress conditions in Arabidopsis thaliana: Col-0 ecotype (wild-type and vtc-2), expressing mitochondrial and cytosolic roGFP1.

Using Arabidopsis plants Col-0 and vtc2 transformed with a redox sensitive green fluorescent protein, (c-roGFP) and (m-roGFP), we investigated the effects of a progressive water stress and re-watering on the redox status of the cytosol and the mitochondria. Our results establish that water stress affects redox status differently in these two compartments, depending on phenotype and leaf age, furthermore we conclude that ascorbate plays a pivotal role in mediating redox status homeostasis and that Col-0 Arabidopsis subjected to water stress increase the synthesis of ascorbate suggesting that ascorbate may play a role in buffering changes in redox status in the mitochondria and the cytosol, with the presumed buffering capacity of ascorbate being more noticeable in young compared with mature leaves. Re-watering of water-stressed plants was paralleled by a return of both the redox status and ascorbate to the levels of well-watered plants. In contrast to the effects of water stress on ascorbate levels, there were no significant changes in the levels of glutathione, thereby suggesting that the regeneration and increase in ascorbate in water-stressed plants may occur by other processes in addition to the regeneration of ascorbate via the glutathione. Under water stress in vtc2 lines it was observed stronger differences in redox status in relation to leaf age, than due to water stress conditions compared with Col-0 plants. In the vtc2 an increase in DHA was observed in water-stressed plants. Furthermore, this work confirms the accuracy and sensitivity of the roGFP1 biosensor as a reporter for variations in water stress-associated changes in redox potentials.

CLE genes may act in a variety of tissues/cells and involve other signaling cascades in addition to CLV3-WUS-like pathways.

CLE, which is the term for the CLV3/ESR-related gene family, is thought to participate in CLAVATA3-WUSCHEL (CLV3-WUS) and CLV3-WUS-like signaling pathways to regulate meristem activity in plant. Although some CLE genes are expressed in meristems, many CLE genes appear to express in a variety of tissues/cells. Here we report that CLE14 and CLE20 express in various specific tissues/cells outside the shoot/root apical meristem (SAM/RAM), including in highly differentiated cells, and at different developmental stages. Over-expressing CLE14 or CLE20 also causes multiple phenotypes, which is consistent with its expression pattern in Arabidopsis. These results suggest that CLE genes may play multiple roles and involve other signaling cascades in addition to the CLV3-WUS and CLV3-WUS-like pathways.

Redox regulation of root apical meristem organization: connecting root development to its environment.

Post-embryonic root growth relies on the proliferative activity of the root apical meristem (RAM), consisting, in part, of cells with juvenile characteristics (stem cells). It is generally, but erroneously held that the RAM indefinitely produces new cells throughout the lifespan of a plant, resulting in indeterminate root growth. On the contrary, convincing data, mainly from the lab of Thomas L. Rost, show in all species analyzed so far, including Arabidopsis, that RAM organization changes over time in parallel with both a cessation of the production of new cells, and a consequent reduction in root growth, even under optimal conditions. In addition, RAM organization evolved to become highly plastic and dynamic in response to environmental triggers (e.g. water and nutrient availability, pollutants). Under unfavourable conditions, the RAM is rapidly reorganized, and, as a result of the cessation of new cell production at the root tip, root growth is altered, and lateral root production is enhanced, thus providing the plant additional strategies to overcome the stress. It is now becoming increasingly clear that this environment-responsive developmental plasticity is linked to reactive oxygen/nitrogen species, antioxidants, and related enzymes, which form part of a complex signalling module specifically operating in the regulation of RAM functioning, in strict relationship with hormonal control of root development exerted by auxin, gibberellins and cytokinins. In turn, such redox/hormone crosstalk regulates gene expression.

Transcription profile analyses identify genes and pathways central to root cap functions in maize.

Affymetrix GeneChips arrayed with about one-half (~23K) of the rice genes were used to profile gene transcription activity in three tissues comprising the maize root tip; the proximal meristem (PM), the quiescent center (QC), and the root cap (RC). Here we analyze the gene transcription profile of the RC, compared to both the PM and the QC, from three biological replicates. In the RC, a total of 669 genes were identified as being differentially upregulated, and 365 differentially downregulated. Real-time quantitative RT-PCR analysis was used to confirm upregulated genes in the RC. In addition, using the technique of laser microdissection (LMD) we localized upregulated gene expression to the lateral RC cells. Taken as a whole, transcription profile analyses revealed the upregulation in the maize RC of clusters of genes linked to major metabolic processes and pathways, including: (1) transport, both the export of carbohydrates and the uptake of nutrients; (2) sensing and responding to (often stressful) biotic and abiotic environmental stimuli; (3) integrating the responses of at least 3 major growth regulators (auxin, ethylene, jasmonic acid); (4) processing the large amount of carbohydrate transported into the RC. Although the profile data are derived using heterologous rice GeneChips, with about half of the total rice gene set, this study, nevertheless, provides a genomic scale characterization of the entire RC, and serves as a new platform from which to advance studies of the network of pathways operating in the maize RC.

Regulation of root apical meristem development.

The establishment of the Angiosperm root apical meristem is dependent on the specification of a stem cell niche and the subsequent development of the quiescent center at the presumptive root pole. Distribution of auxin and the establishment of auxin maxima are early formative steps in niche specification that depend on the expression and distribution of auxin carriers. Auxin specifies stem cell niche formation by directly and indirectly affecting gene activities. Part of the indirect regulation by auxin may involve changes in redox, favoring local, oxidized microenvironments. Formation of a QC is required for root meristem development and elaboration. Many signals likely pass between the QC and the adjacent root meristem tissues. Disappearance of the QC is associated with roots becoming determinate. Given the many auxin feedback loops, we hypothesize that roots evolved as part of an auxin homeostasis mechanism.

Auxin and ethylene interactions control mitotic activity of the quiescent centre, root cap size, and pattern of cap cell differentiation in maize.

Root caps (RCs) are the terminal tissues of higher plant roots. In the present study the factors controlling RC size, shape and structure were examined. It was found that this control involves interactions between the RC and an adjacent population of slowly dividing cells, the quiescent centre, QC. Using the polar auxin transport inhibitor 1-N-naphthylphthalamic acid (NPA), the effects of QC activation on RC gene expression and border cell release was characterized. Ethylene was found to regulate RC size and cell differentiation, since its addition, or the inhibition of its synthesis, affected RC development. The stimulation of cell division in the QC following NPA treatment was reversed by ethylene, and quiescence was re-established. Moreover, inhibition of both ethylene synthesis and auxin polar transport triggered a new pattern of cell division in the root epidermis and led to the appearance of supernumerary epidermal cell files with cap-like characteristics. The data suggest that the QC ensures an ordered internal distribution of auxin, and thereby regulates not only the planes of growth and division in both the root apex proper and the RC meristem, but also regulates cell fate in the RC. Ethylene appears to regulate the auxin redistribution system that resides in the RC. Experiments with Arabidopsis roots also reveal that ethylene plays an important role in regulating the auxin sink, and consequently cell fate in the RC.

VIZARD: analysis of Affymetrix Arabidopsis GeneChip data.

UNLABELLED: The Affymetrix GeneChip Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip array. AVAILABILITY: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/ CONTACT: moseyko@uclink4.berkeley.edu