The use of chemical genomics to investigate pathways intersecting auxin-dependent responses and endomembrane trafficking in Arabidopsis thaliana

Endocytic trafficking induces lateral root founder cell specification in Arabidopsis thaliana in a process distinct from the auxin-induced pathway

Plants can modify their body structure, such as their root architecture, post-embryonically. For example, Arabidopsis thaliana can develop lateral roots as part of an endogenous program or in response to biotic and abiotic stimuli. Root pericycle cells are specified to become lateral root founder cells, initiating lateral root organogenesis. We used the endocytic trafficking inducer Sortin2 to examine the role of endomembrane trafficking in lateral root founder cell specification. Our results indicate that Sortin2 stimulation turns on a de novo program of lateral root primordium formation that is distinct from the endogenous program driven by auxin. In this distinctive mechanism, extracellular calcium uptake and endocytic trafficking toward the vacuole are required for lateral root founder cell specification upstream of the auxin module led by AUX/IAA28. The auxin-dependent TIR1/AFB F-boxes and auxin polar transport are dispensable for the endocytic trafficking-dependent lateral root founder cell specification; however, a different set of F-box proteins and a functional SCF complex are required. The endocytic trafficking could constitute a convenient strategy for organogenesis in response to environmental conditions.

Novel small molecule modulators of plant growth and development identified by high-content screening with plant pollen

BACKGROUND

Small synthetic molecules provide valuable tools to agricultural biotechnology to circumvent the need for genetic engineering and provide unique benefits to modulate plant growth and development.

RESULTS

We developed a method to explore molecular mechanisms of plant growth by high-throughput phenotypic screening of haploid populations of pollen cells. These cells rapidly germinate to develop pollen tubes. Compounds acting as growth inhibitors or stimulators of pollen tube growth are identified in a screen lasting not longer than 8 h high-lighting the potential broad applicability of this assay to prioritize chemicals for future mechanism focused investigations in plants. We identified 65 chemical compounds that influenced pollen development. We demonstrated the usefulness of the identified compounds as promotors or inhibitors of tobacco and Arabidopsis thaliana seed growth. When 7 days old seedlings were grown in the presence of these chemicals twenty two of these compounds caused a reduction in Arabidopsis root length in the range from 4.76 to 49.20 % when compared to controls grown in the absence of the chemicals. Two of the chemicals sharing structural homology with thiazolidines stimulated root growth and increased root length by 129.23 and 119.09 %, respectively. The pollen tube growth stimulating compound (S-02) belongs to benzazepin-type chemicals and increased Arabidopsis root length by 126.24 %.

CONCLUSIONS

In this study we demonstrate the usefulness of plant pollen tube based assay for screening small chemical compound libraries for new biologically active compounds. The pollen tubes represent an ultra-rapid screening tool with which even large compound libraries can be analyzed in very short time intervals. The broadly applicable high-throughput protocol is suitable for automated phenotypic screening of germinating pollen resulting in combination with seed germination assays in identification of plant growth inhibitors and stimulators.

Computational insight into the chemical space of plant growth regulators

An enormous technological progress has resulted in an explosive growth in the amount of biological and chemical data that is typically multivariate and tangled in structure. Therefore, several computational approaches have mainly focused on dimensionality reduction and convenient representation of high-dimensional datasets to elucidate the relationships between the observed activity (or effect) and calculated parameters commonly expressed in terms of molecular descriptors. We have collected the experimental data available in patent and scientific publications as well as specific databases for various agrochemicals. The resulting dataset was then thoroughly analyzed using Kohonen-based self-organizing technique. The overall aim of the presented study is to investigate whether the developed in silico model can be applied to predict the agrochemical activity of small molecule compounds and, at the same time, to offer further insights into the distinctive features of different agrochemical categories. The preliminary external validation with several plant growth regulators demonstrated a relatively high prediction power (67%) of the constructed model. This study is, actually, the first example of a large-scale modeling in the field of agrochemistry.

Arabidopsis ribosomal proteins control vacuole trafficking and developmental programs through the regulation of lipid metabolism

The vacuole is the most prominent compartment in plant cells and is important for ion and protein storage. In our effort to search for key regulators in the plant vacuole sorting pathway, ribosomal large subunit 4 (rpl4d) was identified as a translational mutant defective in both vacuole trafficking and normal development. Polysome profiling of the rpl4d mutant showed reduction in polysome-bound mRNA compared with wild-type, but no significant change in the general mRNA distribution pattern. Ribsomal profiling data indicated that genes in the lipid metabolism pathways were translationally down-regulated in the rpl4d mutant. Live imaging studies by Nile red staining suggested that both polar and nonpolar lipid accumulation was reduced in meristem tissues of rpl4d mutants. Pharmacological evidence showed that sterol and sphingolipid biosynthetic inhibitors can phenocopy the defects of the rpl4d mutant, including an altered vacuole trafficking pattern. Genetic evidence from lipid biosynthetic mutants indicates that alteration in the metabolism of either sterol or sphingolipid biosynthesis resulted in vacuole trafficking defects, similar to the rpl4d mutant. Tissue-specific complementation with key enzymes from lipid biosynthesis pathways can partially rescue both vacuole trafficking and auxin-related developmental defects in the rpl4d mutant. These results indicate that lipid metabolism modulates auxin-mediated tissue differentiation and endomembrane trafficking pathways downstream of ribosomal protein function.

The use of multidrug approach to uncover new players of the endomembrane system trafficking machinery

Chemical Biology is a strong tool to perform experimental procedures to study the Endomembrane System (ES) in plant biology. In the last few years, several bioactive compounds and their effects upon protein trafficking as well as organelle distribution, identity, and size in plants and yeast have been characterized. Today, several of these chemical tools are widely used to perform mutant screens and establish the trafficking pathway of a given cellular component. This chapter is a guideline to perform multidrug approaches to study the endomembrane system in plant cells. This type of approach is a powerful and useful strategy to thoroughly determine the trafficking of a specific protein as well as to perform mutant screens based on phenotypes produced by drug treatments. On the other hand, a multidrug approach can address the characterization of a new bioactive molecule and find its cellular pathway target. Overall, this approach can unravel mechanisms and identify new players in endomembrane trafficking.

Endocytic trafficking towards the vacuole plays a key role in the auxin receptor SCF(TIR)-independent mechanism of lateral root formation in A. thaliana

Plants' developmental plasticity plays a pivotal role in responding to environmental conditions. One of the most plastic plant organs is the root system. Different environmental stimuli such as nutrients and water deficiency may induce lateral root formation to compensate for a low level of water and/or nutrients. It has been shown that the hormone auxin tunes lateral root development and components for its signaling pathway have been identified. Using chemical biology, we discovered an Arabidopsis thaliana lateral root formation mechanism that is independent of the auxin receptor SCF(TIR). The bioactive compound Sortin2 increased lateral root occurrence by acting upstream from the morphological marker of lateral root primordium formation, the mitotic activity. The compound did not display auxin activity. At the cellular level, Sortin2 accelerated endosomal trafficking, resulting in increased trafficking of plasma membrane recycling proteins to the vacuole. Sortin2 affected Late endosome/PVC/MVB trafficking and morphology. Combining Sortin2 with well-known drugs showed that endocytic trafficking of Late E/PVC/MVB towards the vacuole is pivotal for Sortin2-induced SCF(TIR)-independent lateral root initiation. Our results revealed a distinctive role for endosomal trafficking in the promotion of lateral root formation via a process that does not rely on the auxin receptor complex SCF(TIR).

Advances in dissecting endomembrane trafficking with small molecules

Chemical genomics is relatively new to plant biology in academia; however, the ability of this approach to present novel discoveries is being demonstrated clearly. One particularly suitable application of this approach is plant endomembrane trafficking. The rapid and dynamic nature of vesicular trafficking plus genetic redundancy has hampered effective study of this complex network. The ability of small molecules to act quickly to inhibit or arrest vesicular trafficking should permit the association of specific vesicles, especially endosome compartments, with their cargoes, particularly those destined for the plasma membrane. This approach and the large target space presented by the endomembrane trafficking network require the discovery of many new bioactive molecules. Advances in high-throughput chemical screening in plants are making this a reality. However, successful chemical genomic approaches in plants must be coupled with improvements in automated microscopy, image analysis, and target identification. In addition, the ability to correlate specific molecules with complex phenotypic data will be crucial. The data obtained from these experiments will be composed of a matrix of intracellular markers displaying complex chemically induced phenotypes as well as whole plant and perhaps data generated by genomics, proteomics, and metabolomics. In this manner, it should be possible to view endomembrane trafficking and its interactions as a systems-based network.

Identification of an ABCB/P-glycoprotein-specific inhibitor of auxin transport by chemical genomics

Plant development and physiology are widely determined by the polar transport of the signaling molecule auxin. This process is controlled on the cellular efflux level catalyzed by members of the PIN (pin-formed) and ABCB (ATP-binding cassette protein subfamily B)/P-glycoprotein family that can function independently and coordinately. In this study, we have identified by means of chemical genomics a novel auxin transport inhibitor (ATI), BUM (2-[4-(diethylamino)-2-hydroxybenzoyl]benzoic acid), that efficiently blocks auxin-regulated plant physiology and development. In many respects, BUM resembles the functionality of the diagnostic ATI, 1-N-naphtylphtalamic acid (NPA), but it has an IC(50) value that is roughly a factor 30 lower. Physiological analysis and binding assays identified ABCBs, primarily ABCB1, as key targets of BUM and NPA, whereas PIN proteins are apparently not directly affected. BUM is complementary to NPA by having distinct ABCB target spectra and impacts on basipetal polar auxin transport in the shoot and root. In comparison with the recently identified ATI, gravacin, it lacks interference with ABCB membrane trafficking. Individual modes or targets of action compared with NPA are reflected by apically shifted root influx maxima that might be the result of altered BUM binding preferences or affinities to the ABCB nucleotide binding folds. This qualifies BUM as a valuable tool for auxin research, allowing differentiation between ABCB- and PIN-mediated efflux systems. Besides its obvious application as a powerful weed herbicide, BUM is a bona fide human ABCB inhibitor with the potential to restrict multidrug resistance during chemotherapy.

Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases

A previously undescribed forward chemical genetic screen using hydrolases affecting the extracellular matrix is introduced. The developed screen takes advantage of the power of chemical genetics and combines it with the known substrate specificity of glycosylhydrolases, resulting in the selection of conditional mutants that exhibit structural defects in their extracellular matrix. Identification of the responsible genetic locus in those mutants significantly extends our knowledge of genes involved in the biosynthesis, metabolism, signaling, and functionality of components of the extracellular matrix. The method is exemplified by a screen of mutagenized Arabidopsis plants subjected to growth in liquid culture in the presence of a xyloglucanase, an enzyme acting on the major cross-linking glycan found in the extracellular matrix of this plant. Using this hydrolase-based screen, dozens of plant cell wall mutants (xeg mutants) were identified, leading to the identification of 23 genetic loci that affect plant cell walls. One of the identified loci is XEG113, encoding a family 77 glycosyltransferase (GT77). Detailed analysis of the wall of this mutant indicated that its extensins, structural glyocoproteins present in walls, are underarabinosylated. Xeg-113 plants exhibit more elongated hypocotyls than WT, providing genetic evidence that plant O-glycosylation--more specifically, extensin arabinosylation--is important for cell elongation.