New methods to analyse auxin-induced growth I: Classical auxinology goes Arabidopsis

During recent years, genetic approaches have become invaluable tools to analyse signalling chains in plants. The first step to understand auxin signalling is the isolation of signal transduction mutants. In Arabidopsis, screening for auxin resistant plants has identified a number of mutants. However, it is difficult to link the mutated genes to the rapid growth response to auxin. As yet, there is no published method to measure auxin-induced growth at a sufficient temporal resolution. A novel auxanometer described here will close that gap. Hypocotyl segments are immersed in buffer in a flow-through cuvette. A CCD-camera attached to a microscope is used to image markings on the hypocotyl surfaces and to track their movements across the field of view.To illustrate the applicability of this method for analysing mutants we compared the growth responses of tomato wild type with the mutant diageotropica (dgt). We showed that the mutation completely abolished all phases of the rapid growth reaction to applied auxin. This excludes the possibility that the reduced auxin sensitivity reported in the literature is due to a reduced or delayed response. Our technique was modified for use with the tiny Arabidopsis thaliana hypocotyl segments and inflorescence stems. In both systems auxin induced a growth response after a lag phase of 15–20 minutes. The new method will now be used to characterise the physiological effect of the mutations in auxin signalling.     

Experimental and computational approaches for the study of calmodulin interactions

Ca²⁺, a universal messenger in eukaryotes, plays a major role in signaling pathways that control many growth and developmental processes in plants as well as their responses to various biotic and abiotic stresses. Cellular changes in Ca²⁺ in response to diverse signals are recognized by protein sensors that either have their activity modulated or that interact with other proteins and modulate their activity. Calmodulins (CaMs) and CaM-like proteins (CMLs) are Ca²⁺ sensors that have no enzymatic activity of their own but upon binding Ca²⁺ interact and modulate the activity of other proteins involved in a large number of plant processes. Protein-protein interactions play a key role in Ca²⁺/CaM-mediated in signaling pathways. In this review, using CaM as an example, we discuss various experimental approaches and computational tools to identify protein-protein interactions. During the last two decades hundreds of CaM-binding proteins in plants have been identified using a variety of approaches ranging from simple screening of expression libraries with labeled CaM to high-throughput screens using protein chips. However, the high-throughput methods have not been applied to the entire proteome of any plant system. Nevertheless, the data provided by these screens allows the development of computational tools to predict CaM-interacting proteins. Using all known binding sites of CaM, we developed a computational method that predicted over 700 high confidence CaM interactors in the Arabidopsis proteome. Most (>600) of these are not known to bind calmodulin, suggesting that there are likely many more CaM targets than previously known. Functional analyses of some of the experimentally identified Ca²⁺ sensor target proteins have uncovered their precise role in Ca²⁺-mediated processes. Further studies on identifying novel targets of CaM and CMLs and generating their interaction network - “calcium sensor interactome” - will help us in understanding how Ca²⁺ regulates a myriad of cellular and physiological processes.     

Digital image analysis of expansion growth of cultured cotton ovules with fibers and their responses to ABA

Cotton ovule cultures have obvious advantages over whole plants when experimental protocols call for inhibitors, radio-labeled precursors or controlled environmental conditions to be tested. The responses of ovule expansion growth and attached fiber elongation to external factors require accurate measurement techniques. This paper presents a new method for digital image analysis of the growth area of cotton ovules with fibers at high resolution. The method was characterized under constant conditions and during dynamic responses to different levels of ABA (abscisic acid) treatment. The growth area was treated as area occupied within the outline of the Petri dish image of the growing ovule with fibers. Growth area increase showed the same trends as fiber length increase and was significantly correlated with the fiber length increase under different levels of ABA treatment (r ² = 0.97). This new analysis method provides a simple, noninvasive, and more accurate approach for growth analysis in the cotton ovule culture system. Using this method, the effects of ABA on expansion growth of ovule with fibers were characterized.     

Stress and aberrant phenotypes in vitro culture

Stress responses are largely conserved in eukaryotic cells, but with plants having certain distinctive reactions to specific stresses, e.g. the induction of pathogenesis-related proteins. General responses to stress involve signaling stress detection via the redox system, checkpoints arresting the cell cycle and DNA repair processes stimulated in response to DNA damage. Specific responses to stress include the induction of protective metabolites, such as betaines, and protective proteins, for example, heat shock proteins. Chemical signals, e.g. reactive oxygen species, Ca²⁺ and plant hormones, acting through signal transduction cascades activate genomic re-programming. Genome plasticity in plants allows adaptation to environmental conditions and includes genomic or epigenetic changes (histone acetylation, methylation, chromatin remodeling etc.) and possibly directed mutation. In plants, recent research has indicated that intricate stress response mechanisms and `cross talk' between stress responses exist. Here, changes in the plant genome and in genomic expression in development and as a response to environmental stress are reviewed as background to a discussion of the basis of aberrant genomic expression in vitro. Markers are discussed which may be used to characterize the stress exposure of in vitro tissues.     

Separation of early and late responses to herbivory in Arabidopsis by changing plasmodesmal function

Herbivory results in an array of physiological changes in the host that are separable from the associated physical damage. We have made the surprising observation that an Arabidopsis line (pdko3) mutated in genes encoding plasmodesmal proteins is defective in some, but not all, of the typical plant responses to herbivory. We tested the responses of plasma transmembrane potential (Vm) depolarization, voltage gated K⁺ channel activity, cytosolic calcium [Ca²⁺]_cyt and reactive oxygen species (ROS) (H₂O₂ and NO) release, shoot‐to‐root signaling, biosynthesis of the phytohormone jasmonic acid (JA) and the elicitation of volatile organic compounds (VOCs). Following herbivory and the release of factors present in insect oral secretions (including a putative β‐galactofuranose polysaccharide), both the pdko3 and wild type (WT) plants showed a increased accumulation of [Ca²⁺]_cyt, NO and H₂O₂. In contrast, unlike WT plants, the mutant line showed an almost complete loss of voltage gated K⁺ channel activity and Vm depolarization, a loss of shoot‐induced root‐Vm depolarization, a loss of activation and regulation of gene expression of the JA defense pathway, and a much diminished release and altered profile of VOCs. The mutations in genes for plasmodesmal proteins have provided valuable genetic tools for the dissection of the complex spectrum of responses to herbivory and shown us that the responses to herbivory can be separated into a calcium‐activated oxidative response and a K⁺‐dependent Vm‐activated jasmonate response associated with the release of VOCs.     

2D electrophoresis-based expression proteomics: a microbiologist’s perspective

Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist’s perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.     

How mathematical modelling elucidates signalling in Bacillus subtilis

Appropriate stimulus perception, signal processing and transduction ensure optimal adaptation of bacteria to environmental challenges. In the Gram‐positive model bacterium Bacillus subtilis signalling networks and molecular interactions therein are well‐studied, making this species a suitable candidate for the application of mathematical modelling. Here, we review systems biology approaches, focusing on chemotaxis, sporulation, σ^B‐dependent general stress response and competence. Processes like chemotaxis and Z‐ring assembly depend critically on the subcellular localization of proteins. Environmental response strategies, including sporulation and competence, are characterized by phenotypic heterogeneity in isogenic cultures. The examples of mathematical modelling also include investigations that have demonstrated how operon structure and signalling dynamics are intricately interwoven to establish optimal responses. Our review illustrates that these interdisciplinary approaches offer new insights into the response of B. subtilis to environmental challenges. These case studies reveal modelling as a tool to increase the understanding of complex systems, to help formulating hypotheses and to guide the design of more directed experiments that test predictions.     

Salt stress tolerance; what do we learn from halophytes?

Abiotic environmental stresses can give rise to morphological, biochemical and molecular changes that negatively affect plant growth and productivity. Among these stresses, soil salinity is the major threat. To deal and control effects of high salinity on plants, it is important to understand their responses to salt stress that disturbs the homeostatic equilibrium at cellular and molecular levels. In this regard halophytes (salt tolerant plants) can provide superior models for the study of salt stress defense parameters compared to salt sensitive species (glycophytes). Halophytes use highly developed, complex systems to tolerate salinity by maintaining a low cytosolic Na⁺/K⁺ ratio, sequestration of Na⁺ into vacuoles that then provides the osmotic potential sustaining water influx. Under low intensity stress conditions that moderately and/or transiently affect ion imbalance, the set of responses all plants initiate will be mostly to engage measures that assure ion balance. High salinity, especially over a prolonged time period, will challenge plant survival, which then requires different strategies that employ a variety of mechanisms. Plasticity and connectivity of these diverse mechanisms is engrained in species- and family-specific evolutionary history and their genetic complexity. Highlighting differences in the genetic and biochemical makeup between glycophytes and halophytes allows for comparisons between their approaches towards high salinity. This review provides a brief overview about different strategies and mechanism used by plants to avoid or confine adverse effects of high salinity.     

Approaches to Ecological Risk Characterization and Management: Selecting the Right Tools for the Job

Chemical-specific hazard quotient (HQ) risk characterization in ecological risk assessment (ERA) can be a value-added tool for risk management decision-making at chemical release sites, when applied appropriately. However, there is little consensus regarding how HQ results can be used for risk management decision-making at the population, community, and ecosystem levels. Furthermore, stakeholders are reluctant to consider alternatives to HQ results for risk management decisions. Chemical-specific HQs risk characterization should be viewed as only one of several approaches (i.e., tools) for addressing ecological issues; and in many situations, other quantitative and qualitative approaches will likely result in superior risk management decisions. The purpose of this paper is to address fundamental issues and limitations associated with chemical-specific HQ risk characterization in ERA, to identify when it may be appropriate, to explore alternatives that are currently available, and to identify areas that could be developed for the future. Several alternatives (i.e., compensatory restoration, performance-based ecological monitoring, ecological significance criteria, net environmental benefit analysis), including their limitations, that can supplement, augment, or substitute for HQs in ERA are presented. In addition, areas of research (i.e., wildlife habitat assessment/landscape ecology/population biology, and field validated risk-based screening levels) that could yield new tools are discussed.     

Environmental regulation of stomatal response in the <Emphasis Type="Italic">Arabidopsis</Emphasis> Cvi-0 ecotype

The Arabidopsis Cape Verde Islands (Cvi-0) ecotype is known to differ from other ecotypes with respect to environmental stress responses. We analyzed the stomatal behavior of Cvi-0 plants, in response to environmental signals. We investigated the responses of stomatal conductance and aperture to high [CO₂] in the Cvi-0 and Col-0 ecotypes. Cvi-0 showed constitutively higher stomatal conductance and more stomatal opening than Col-0. Cvi-0 stomata opened in response to light, but the response was slow. Under low humidity, stomatal opening was increased in Cvi-0 compared to Col-0. We then assessed whether low humidity affects endogenous ABA levels in Cvi-0. In response to low humidity, Cvi-0 had much higher ABA levels than Col-0. However, epidermal peels experiments showed that Cvi-0 stomata were insensitive to ABA. Measurements of organic and inorganic ions in Cvi-0 guard cell protoplasts indicated an over-accumulation of osmoregulatory anions (malate and Cl⁻). This irregular anion homeostasis in the guard cells may explain the constitutive stomatal opening phenotypes of the Cvi-0 ecotype, which lacks high [CO₂]-induced and low humidity-induced stomatal closure.     

Elevated atmospheric CO2 alters stomatal responses to variable sunlight in a C4 grass

Native tallgrass prairie in NE Kansas was exposed to elevated (twice ambient) or ambient atmospheric CO₂ levels in open-top chambers. Within chambers or in adjacent unchambered plots, the dominant C₄ grass, Andropogon gerardii, was subjected to fluctuations in sunlight similar to that produced by clouds or within canopy shading (full sun > 1500 μmol m⁻² s⁻¹ versus 350 μmol m⁻² s⁻¹ shade) and responses in gas exchange were measured. These field experiments demonstrated that stomatal conductance in A. gerardii achieved new steady state levels more rapidly after abrupt changes in sunlight at elevated CO₂ when compared to plants at ambient CO₂. This was due primarily to the 50% reduction in stomatal conductance at elevated CO₂, but was also a result of more rapid stomatal responses. Time constants describing stomatal responses were significantly reduced (29–33%) at elevated CO₂. As a result, water loss was decreased by as much as 57% (6.5% due to more rapid stomatal responses). Concurrent increases in leaf xylem pressure potential during periods of sunlight variability provided additional evidence that more rapid stomatal responses at elevated CO₂ enhanced plant water status. CO₂-induced alterations in the kinetics of stomatal responses to variable sunlight will likely enhance direct effects of elevated CO₂ on plant water relations in all ecosystems.     

Chloroplast movements in fern leaves: correlation of movement dynamics and environmental flexibility of the species

The movements of chloroplasts in response to varying levels and wavelengths of incident light were investigated in leaves of four fern species: Adiantum capillus-veneris, Adiantum caudatum, Adiantum diaphanum and Pteris cretica. In all of the species studied blue light induced chloroplast redistribution resulting in face and profile patterns that were typical of low and high fluence rates, respectively. Fluence rate response characteristics and the kinetics of transmission changes accompanying these blue-light-induced movements were similar to those observed in the leaves of higher plants. Only in A. capillus-veneris was the distribution of chloroplasts affected by red light. The response was of the weak-light type, irrespective of the light intensity. The most effective fluence rate for red light was found to be below 7·2 μmol m^–2 s^–1 (1 W m^–2). The effect of red light was far-red reversible, indicating phytochrome involvement. Chloroplast responses were more dynamic in A. capillus-veneris and P. cretica, the two species that exhibited higher environmental flexibility.     

RNAi Phenotypes and the Localization of a Protein::GUS Fusion Imply a Role for Medicago truncatula PIN Genes in Nodulation

The symbiosis between legumes and rhizobia results in the development of a new plant organ, the nodule. A role for polar auxin transport in nodule development in Medicago truncatula has been demonstrated using molecular genetic tools. The expression of a DR5::GUS auxin-responsive promoter in uninoculated M. truncatula roots mirrored that reported in Arabidopsis, and expression of the construct in nodulating roots confirmed results reported in white clover. The localization of a root-specific PIN protein (MtPIN2) in normal roots, developing lateral roots and nodules provided the first evidence that a PIN protein is expressed in nodules. Reduced levels of MtPIN2, MtPIN3, and MtPIN4 mRNAs via RNA interference demonstrated that plants with reduced expression of various MtPINs display a reduced number of nodules. The reported results show that in M. truncatula, PIN proteins play an important role in nodule development, and that nodules and lateral roots share some early auxin responses in common, but they rapidly differentiate with respect to auxin and MtPIN2 protein distribution.     

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.     

碱蓬属植物耐盐机理研究进展

碱蓬属(Suaeda)植物是一类典型的真盐生植物,属于重要的盐生植物资源,全球广泛分布.人们已经对20种碱蓬属植物进行了观察和盐胁迫实验,研究了不同器官或组织的生理生化特征及其对盐胁迫的反应,并基于这些研究分析了盐胁迫的应答机制.叶片肉质化、细胞内离子区域化、渗透调节物质增加和抗氧化系统能力增强是碱蓬属植物响应和适应盐胁迫的重要方式和途径.但迄今为止的研究工作尚有一定的局限性,主要包括:研究工作主要集中在植物地上部分,而对植物地下部分的研究较少;多是少数生物学指标或生理学现象的单独观察,而缺乏对生理代谢过程的整体和综合分析;针对某种碱蓬的独立分析较多,而与近缘种的比较研究较少;植物对中性盐胁迫的反应研究较多,而对碱性盐的研究较少.为进一步系统阐明碱蓬属植物的耐盐机制,今后的工作应注重碱蓬属植物响应和适应盐胁迫的信号网络和调控机制研究,基于系统生物学研究思路,采用现代组学技术探索该属植物响应盐胁迫的由复杂信号网络调控的特殊生理特征和特异代谢途径.