Flux-based transport enhancement as a plausible unifying mechanism for auxin transport in meristem development

Plants continuously generate new organs through the activity of populations of stem cells called meristems. The shoot apical meristem initiates leaves, flowers, and lateral meristems in highly ordered, spiralled, or whorled patterns via a process called phyllotaxis. It is commonly accepted that the active transport of the plant hormone auxin plays a major role in this process. Current hypotheses propose that cellular hormone transporters of the PIN family would create local auxin maxima at precise positions, which in turn would lead to organ initiation. To explain how auxin transporters could create hormone fluxes to distinct regions within the plant, different concepts have been proposed. A major hypothesis, canalization, proposes that the auxin transporters act by amplifying and stabilizing existing fluxes, which could be initiated, for example, by local diffusion. This convincingly explains the organised auxin fluxes during vein formation, but for the shoot apical meristem a second hypothesis was proposed, where the hormone would be systematically transported towards the areas with the highest concentrations. This implies the coexistence of two radically different mechanisms for PIN allocation in the membrane, one based on flux sensing and the other on local concentration sensing. Because these patterning processes require the interaction of hundreds of cells, it is impossible to estimate on a purely intuitive basis if a particular scenario is plausible or not. Therefore, computational modelling provides a powerful means to test this type of complex hypothesis. Here, using a dedicated computer simulation tool, we show that a flux-based polarization hypothesis is able to explain auxin transport at the shoot meristem as well, thus providing a unifying concept for the control of auxin distribution in the plant. Further experiments are now required to distinguish between flux-based polarization and other hypotheses.     

AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis

In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.     

A putative mechanism for bog patterning

The surface of bogs commonly shows various spatial vegetation patterning. Typical are "string patterns" consisting of regular densely vegetated bands oriented perpendicular to the slope. Here, we report on regular "maze patterns" on flat ground, consisting of bands densely vegetated by vascular plants in a more sparsely vegetated matrix of nonvascular plant communities. We present a model reproducing these maze and string patterns, describing how nutrient-limited vascular plants are controlled by, and in turn control, both hydrology and solute transport. We propose that the patterns are self-organized and originate from a nutrient accumulation mechanism. In the model, this is caused by the convective transport of nutrients in the groundwater toward areas with higher vascular plant biomass, driven by differences in transpiration rate. In a numerical bifurcation analysis we show how the maze patterns originate from the spatially homogeneous equilibrium and how this is affected by changes in rainfall, nutrient input, and plant properties. Our results confirm earlier model results, showing that redistribution of a limiting resource may lead to fine-scale facilitative and coarse-scale competitive plant interactions in different ecosystems. Self-organization in ecosystems may be a more general phenomenon than previously thought, which can be mechanistically linked to scale-dependent facilitation and competition.     

A plausible mechanism for gene correction by chimeric oligonucleotides

Self-complementary chimeric oligonucleotides that consist of DNA and 2'-O-methyl RNA nucleotides arranged in a double-hairpin configuration can elicit a point mutation when targeted to a gene sequence. We have used a series of structurally diverse chimeric oligonucleotides to correct a mutant neomycin phosphotransferase gene in a human cell-free extract. Analysis of structure-activity relationships demonstrates that the DNA strand of the chimeric oligonucleotide acts as a template for high-fidelity gene correction when one of its bases is mismatched to the targeted gene. By contrast, the chimeric strand of the oligonucleotide does not function as a template for gene repair. Instead, it appears to augment the frequency of gene correction by facilitating complex formation with the target. In the presence of RecA protein, each strand of a chimeric oligonucleotide can hybridize with double-stranded DNA to form a complement-stabilized D-loop. This reaction, which may take place by reciprocal four-strand exchange, is not observed with oligonucleotides that lack 2'-O-methyl RNA segments. Preliminary sequencing data suggest that complement-stabilized D-loops may be weakly mutagenic. If so, a low level of random mutagenesis in the vicinity of the chimera binding site may accompany gene repair.     

A plausible mechanism for large-scale chromosomal DNA amplification in streptomycetes

Recent advances in our understanding of the structure of highly amplified DNA sequences in Streptomyces fradiae and lividans have enabled us to formulate a possible mechanism by which amplification may occur. An essential feature of the model is the generation of an amplification precursor, which comprises a circularised copy of the DNA to be amplified, attached to one arm of the chromosome by a replication fork. Multiple copies of the amplifiable DNA are generated by rolling circle replication. The model adequately accounts for many features of gene amplification in these two species, including the tendency for deletions to occur to one side, but not the other, of the amplified DNA.     

Maintenance of embryonic auxin distribution for apical-basal patterning by PIN-FORMED-dependent auxin transport in Arabidopsis

Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.     

A mechanism of respiration-dependent water uptake enhanced by auxin

Summary There are many contradictory observations on the mechanohydraulic relation of growing higher plant cells and tissues. Graphical analysis of the simultaneous equations which govern irreversible wall yielding and water absorption has made more comprehensive the understanding of this relation when relative growth rate is plotted against turgor pressure. It suggests that some respiration-dependent and auxin sensitive process might regulate the difference of osmotic potential between cells and water source. Based on anatomical and electrophysiological knowledge of the pea stem xylem, we propose the wall canal system as the mechanism of respiration-dependent water uptake which is sensitive to auxin. This system consists of the xylem apoplastic walls, the xylem proton pumps, active solute uptake system and cell membranes. In the simplest case, third-order simultaneous differential equations are involved. Numerical analysis showed that net uptake of solutes enables water to be taken up against an opposing gradient of water potential. The behaviour of this wall canal system describes well the mechano-hydraulic relation of enlarging plant cells and tissues. Recent typical, but incompatible, interpretations of this relation are critically discussed based on our model.Abbreviations V the volume of enlarging symplast - the average extensibility of the wall - Pⁱ turgor pressure - Y the yield threshold of the wall - L the relative hydraulic conductance - the solute reflection coefficient of the plasmamembrane - Cⁱ the osmotic concentration of the symplast cells - C^x the osmotic concentration of the xylem vessels - P^x hydrostatic pressure in the xylem vessels - R the gas constant - T absolute temperature - ^o water potential of xylem fluid - ⁱ water potential of symplast cells     

Mathematical model of auxin distribution in the plant root

Regulation of plant growth and development by auxin is mediated by the hormone controlled distribution and dose-dependent mechanisms of its action. A mathematical model is proposed, which described the distribution of auxin in the cells extending along the central axis of the Arabidopsis thaliana root. This model reproduces qualitatively both auxin distribution in cells of the root central axis under the normal conditions and under the conditions of decreased active transport and the recovery of auxin distribution and related meristem restoration during root regeneration after ablation of its tip. Different types of distribution of the auxin concentration over the vertical root axis are described, possible variants of root growth and lateral roots formation are proposed, and biological interpretation is given to different regimes of model behavior.     

A new L-type calcium channel isoform required for normal patterning of the developing neuromuscular junction

One of the earliest steps in the development of the neuromuscular junction (NMJ) is the pre-patterning of acetylcholine receptors (AChR) in the center of muscle fibers. This process has recently been proposed to depend on L-type calcium currents. But its feeble current properties make the skeletal muscle calcium channel (Ca(v)1.1) a poor candidate for this function. Independently a new Ca(v)1.1e splice variant with greatly distinct current properties has been described. But so far this channel lacked a function. Could this orphan channel be responsible for regulating AChR pre-patterning? Here we compare the properties of the two splice variants and argue that the newly discovered variant Ca(v)1.1e, is dominantly expressed at the proper time in development and has the essential current properties to accomplish the proposed role in the formation of the NMJ.     

A new L-type calcium channel isoform required for normal patterning of the developing neuromuscular junction

One of the earliest steps in the development of the neuromuscular junction (NMJ) is the pre-patterning of acetylcholine receptors (AChR) in the center of muscle fibers. This process has recently been proposed to depend on L-type calcium currents. But its feeble current properties make the skeletal muscle calcium channel (Ca_v1.1) a poor candidate for this function. Independently a new Ca_v1.1e splice variant with greatly distinct current properties has been described. But so far this channel lacked a function. Could this orphan channel be responsible for regulating AChR pre-patterning? Here we compare the properties of the two splice variants and argue that the newly discovered variant Ca_v1.1e, is dominantly expressed at the proper time in development and has the essential current properties to accomplish the proposed role in the formation of the NMJ.     

Mathematical model of auxin distribution in the plant root

Auxin regulation of plant growth and development is mediated by controlled distribution of this hormone and dose-dependent mechanisms of its action. A mathematical model is proposed, which describes auxin distribution in the cell array along the root longitudinal axis in Arabidopsis thaliana. The model qualitatively simulates auxin distribution over the longitudinal axis in intact roots, changes in this distribution at decreased auxin transport rates, and restoration of the auxin distribution pattern with subsequent establishment of new root meristem in the course of root regeneration after the ablation of its tip. The model shows the presence of different auxin distribution patterns over the longitudinal root axis and suggests possible scenarios for root growth and lateral root formation. Biological interpretation of different regimes of model behavior is presented.     

Axial patterning in the developing vertebrate inner ear

Axial patterning in the vertebrate inner ear has been studied for over eighty years, and recent work has made great progress towards an understanding of the molecular mechanisms responsible for establishing asymmetries about the otic axes. Tissues extrinsic to the ear provide sources of signalling molecules that are active early in development, at or before otic placode stages, while intrinsic factors interpret these signals to establish and maintain axial pattern. Key features of dorsoventral otic patterning in amniote embryos involve Wnt and Fgf signalling from the hindbrain and Hh signalling from midline tissues (notochord and floorplate). Mutual antagonism between these pathways and their downstream targets within the otic epithelium help to refine and maintain dorsoventral axial patterning in the ear. In the zebrafish ear, the same tissues and signals are implicated, but appear to play a role in anteroposterior, rather than dorsoventral, otic patterning. Despite this paradox, conservation of mechanisms may be higher than is at first apparent.     

A plausible mechanism of electron transfer between quinones in photosynthetic reaction centers

The mechanism of long-range electron transfer between the primary and the secondary quinone of photosynthetic reaction centers has been investigated, with particular attention on the role of the iron-histidine bridge. Computations suggest that in such a system, where the molecular subunits are packed together by H-bonds, a mobile electron, injected on one end of the chain, can be carried to the other end by switching the positions of the H-bonded hydrogens. Energy estimates would suggest that the proposed mechanism is plausible and worthy of further experimental investigations.     

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.