Effects of stress on cellular infrastructure and metabolic organization in plant cells

The Comparatively Proteomic Analysis in Response to Cold Stress in Cassava Plantlets

Cassava (Manihot esculenta Crantz) is a tropical root crop and sensitive to low temperature. However, it is poorly to know how cassava can modify its metabolism and growth to adapt to cold stress. An investigation aimed at a better understanding of cold-tolerant mechanism of cassava plantlets was carried out with the approaches of physiology and proteomics in the present study. The principal component analysis of seven physiological characteristics showed that electrolyte leakage (EL), chlorophyll content, and malondialdehyde (MDA) may be the most important physiological indexes for determining cold-resistant abilities of cassava. The genome-wide proteomic analysis showed that 20 differential proteins had the same patterns in the apical expanded leaves of cassava SC8 and Col1046. They were mainly related to photosynthesis, carbon metabolism and energy metabolism, defense, protein synthesis, amino acid metabolism, signal transduction, structure, detoxifying and antioxidant, chaperones, and DNA-binding proteins, in which 40 % were related with photosynthesis. The remarkable variation in photosynthetic activity and expression level of peroxiredoxin is closely linked with expression levels of proteomic profiles. Moreover, analysis of differentially expressed proteins under cold stress is an important step toward further elucidation of mechanisms of cold stress resistance.

Function of metabolic and organelle networks in crowded and organized media

(Macro)molecular crowding and the ability of the ubiquitous cytoskeleton to dynamically polymerize–depolymerize are prevalent cytoplasmic conditions in prokaryotic and eukaryotic cells. Protein interactions, enzymatic or signaling reactions - single, sequential or in complexes - whole metabolic pathways and organelles can be affected by crowding, the type and polymeric status of cytoskeletal proteins (e.g., tubulin, actin), and their imparted organization. The self-organizing capability of the cytoskeleton can orchestrate metabolic fluxes through entire pathways while its fractal organization can frame the scaling of activities in several levels of organization. The intracellular environment dynamics (e.g., biochemical reactions) is dominated by the orderly cytoskeleton and the intrinsic randomness of molecular crowding. Existing evidence underscores the inherent capacity of intracellular organization to generate emergent global behavior. Yet unknown is the relative impact on cell function provided by organelle or functional compartmentation based on transient proteins association driven by weak interactions (quinary structures) under specific environmental challenges or functional conditions (e.g., hypoxia, division, differentiation). We propose a qualitative, integrated structural–functional model of cytoplasmic organization based on a modified version of the Sierspinsky–Menger–Mandelbrot sponge, a 3D representation of a percolation cluster, and examine its capacity to accommodate established experimental facts.

Modeling of sensing potency of cytoskeletal systems decorated with metabolic enzymes

The highly dynamic cytoskeleton interacts with enzymes and other proteins that are involved in metabolic or signaling pathways. These interactions can influence the structural and functional characteristics of the partners at the microscopic level of individual proteins and polymers. In this work the functional consequences of such interactions have been studied at the macroscopic level in order to evaluate the integrative and regulatory roles of the metabolic pathways associated with the microtubule cytoskeleton. Here we present mathematical models of the interactions between a hypothetical metabolic pathway and microtubule assembly, and explore for the first time the functional consequences of these interactions in distinct situations. The models include kinetic constants of the individual steps and testable, relevant parameters which allow the quantification of the coupled processes at the microscopic and macroscopic levels. For example our kinetic model for the self-assembly of microtubules reproduces the alteration of the time-dependent turbidity caused by pyruvate kinase binding. Our data reveal the power of a mechanistic description of a filamentous system to explain how cells sense the state of metabolic and other pathways.

Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)

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Waterlogging adversely affects sugarcane productivity and quality.

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A subtractive cDNA library was prepared from sugarcane leaf tissue and sequenced to generate ESTs.

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EST sequences were used to identify transcripts induced by waterlogging.

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The sequenced clones were classified by predicted functions and stress-related genes formed the largest class.

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EST sequences were also used to identify putative novel microRNAs and their targets.

Sugarcane is an important tropical cash crop meeting 75% of world sugar demand and it is fast becoming an energy crop for the production of bio-fuel ethanol. A considerable area under sugarcane is prone to waterlogging which adversely affects both cane productivity and quality. In an effort to elucidate the genes underlying plant responses to waterlogging, a subtractive cDNA library was prepared from leaf tissue. cDNA clones were sequenced and annotated for their putative functions. Major groups of ESTs were related to stress (15%), catalytic activity (13%), cell growth (10%) and transport related proteins (6%). A few stress-related genes were identified, including senescence-associated protein, dehydration-responsive family protein, and heat shock cognate 70 kDa protein. A bioinformatics search was carried out to discover novel microRNAs (miRNAs) that can be regulated in sugarcane plants subjected to waterlogging stress. Taking advantage of the presence of miRNA precursors in the related sorghum genome, seven candidate mature miRNAs were identified in sugarcane. The application of subtraction technology allowed the identification of differentially expressed sequences and novel miRNAs in sugarcane under waterlogging stress. The comparative global transcript profiling in sugarcane plants undertaken in this study suggests that proteins associated with stress response, signal transduction, metabolic activity and ion transport play important role in conferring waterlogging tolerance in sugarcane.

Comparative gene expression analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticina

Gene expression after leaf rust infection was compared in near-isogenic wheat lines differing in the Lr10 leaf rust resistance gene. RNA from susceptible and resistant plants was used for cDNA library construction. In total, 55 008 ESTs were sequenced from the two libraries, then combined and assembled into 14 268 unigenes for further analysis. Of these ESTs, 89% encoded proteins similar to (E value of < or =10(-5)) characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions, cellular localization and biological processes based on gene ontology classification. Further, the unigenes were classified into susceptible and resistant classes based on the EST members assembled from the respective libraries. Several genes from the resistant sample (14-3-3 protein, wali5 protein, actin-depolymerization factor and ADP-ribosylation factor) and the susceptible sample (brown plant hopper resistance protein, caffeic acid O-methyltransferase, pathogenesis-related protein and senescence-associated protein) were selected and their differential expression in the resistant and susceptible samples collected at different time points after leaf rust infection was confirmed by RT-PCR analysis. The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies.

Reflections on 'plant neurobiology'

Plant neurobiology, a new and developing area in the plant sciences, is a meeting place for scientists concerned with exploring how plants perceive signs within their environment and convert them into internal electro-chemical ('plant neurobiological') signals. These signals, in turn, permit rapid modifications of physiology and development that help plants adjust to changes in their environment. The use of the epithet 'neurobiology' in the context of plant life has, however, led to misunderstanding about the aims, content, and scope of this topic. This difficulty is possibly due to the terminology used, since this is often unfamiliar in the context of plants. In the present article, the scope of plant neurobiology is explored and some of analogical and metaphorical aspects of the subject are discussed. One approach to reconciling possible problems of using the term 'plant neurobiology' and, at the same time, of analysing information transfer in plants and the developmental processes which are regulated thereby, is through Living Systems Theory (LST). This theory specifically directs attention to the means by which information is gathered and processed, and then dispersed throughout the hierarchy of organisational levels of the plant body. Attempts to identify the plant 'neural' structures point to the involvement of the vascular tissue - xylem and phloem - in conveying electrical impulses generated in zones of special sensitivity to receptive locations throughout the plant in response to mild stress. Vascular tissue therefore corresponds, at the level of organismic organisation, with the informational 'channel and net' subsystem of LST.

The Cytomatrix as a Cooperative System of Macromolecular and Water Networks

Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.

Recruitment of myosin VIII towards plastid surfaces is root-cap specific and provides the evidence for actomyosin involvement in root osmosensing

The existence of a cell wall-plasma membrane-cytoskeleton (WMC) continuum in plants has long been postulated. However, the individual molecules building such a continuum are still largely unknown. We test here the hypothesis that the integrin-based multiprotein complexes of animal cells have been replaced in plants with more dynamic entities. Using an experimental approach based on protoplast digestion mixtures, and utilising specific antibodies against Arabidopsis ATM1 myosin, we reveal possible roles played by plant-specific unconventional myosin VIII in the functioning of WMC continuum. We demonstrate rapid relocation (less than 5 min) of myosin VIII to statolith surfaces in maize root-cap cells, which is accompanied by the reorganisation of actin cytoskeleton. Upon prolonged stimulation, myosin VIII is also recruited to plasmodesmata and pit-fields of plasmolysing root cap statocytes. The osmotic stimulus is the major factor inducing relocation, but the cell wall-cytoskeleton interactions also play an important role. In addition, we demonstrate the tight association of myosin VIII with the surfaces of chloroplasts, and provide an indication for the differences in the mechanisms of plastid movement in roots and leaves of plants. Overall, our data provide evidence for the active involvement of actomyosin complexes, rooted in the WMC continuum, in the cellular volume control and maintenance of spatial relationships between cellular compartments.

The fractal architecture of cytoplasmic organization: scaling, kinetics and emergence in metabolic networks

In this work, we highlight the links between fractals and scaling in cells and explore the kinetic consequences for biochemical reactions operating in fractal media. Based on the proposal that the cytoskeletal architecture is organized as a percolation lattice, with clusters emerging as fractal forms, the analysis of kinetics in percolation clusters is especially emphasized. A key consequence of this spatiotemporal cytoplasmic organization is that enzyme reactions following Michaelis-Menten or allosteric type kinetics exhibit higher rates in fractal media (for short times and at lower substrate concentrations) at the percolation threshold than in Euclidean media. As a result, considerably faster and higher amplification of enzymatic activity is obtained. Finally, we describe some of the properties bestowed by cytoskeletal organization and dynamics on metabolic networks.

Ion condensation and signal transduction

Many abiotic and other signals are transduced in eukaryotic cells by changes in the level of free calcium via pumps, channels and stores. We suggest here that ion condensation should also be taken into account. Calcium, like other counterions, is condensed onto linear polymers at a critical value of the charge density. Such condensation resembles a phase transition and has a topological basis in that it is promoted by linear as opposed to spherical assemblies of charges. Condensed counterions are delocalised and can diffuse in the so-called near region along the polymers. It is generally admitted that cytoskeletal filaments, proteins colocalised with these filaments, protein filaments distinct from cytoskeletal filaments, and filamentous assemblies of other macromolecules, constitute an intracellular macromolecular network. Here we draw attention to the fact that this network has physicochemical characteristics that enable counterion condensation. We then propose a model in which the feedback relationships between the condensation/decondensation of calcium and the activation of calcium-dependent kinases and phosphatases control the charge density of the filaments of the intracellular macromolecular network. We show how condensation might help mediate free levels of calcium both locally and globally. In this model, calcium condensation/decondensation on the macromolecular network creates coherent patterns of protein phosphorylation that integrate signals. This leads us to hypothesize that the process of ion condensation operates in signal transduction, that it can have an integrative role and that the macromolecular network serves as an integrative receptor.

The Arabidopsis cytoskeletal genome

In the past decade the first Arabidopsis genes encoding cytoskeletal proteins were identified. A few dozen genes in the actin and tubulin cytoskeletal systems have been characterized thoroughly, including gene families encoding actins, profilins, actin depolymerizing factors, α-tubulins, and β-tubulins. Conventional molecular genetics have shown these family members to be differentially expressed at the temporal and spatial levels with an ancient split separating those genes expressed in vegetative tissues from those expressed in reproductive tissues. A few members of other cytoskeletal gene families have also been partially characterized, including an actin-related protein, annexins, fimbrins, kinesins, myosins, and villins. In the year 2001 the Arabidopsis genome sequence was completed. Based on sequence homology with well-characterized animal, fungal, and protist sequences, we find candidate cytoskeletal genes in the Arabidopsis database: more than 150 actin-binding proteins (ABPs), including monomer binding, capping, cross-linking, attachment, and motor proteins; more than 200 microtubule-associated proteins (MAPs); and, surprisingly, 10 to 40 potential intermediate filament (IF) proteins. Most of these sequences are uncharacterized and were not identified as related to cytoskeletal proteins. Several Arabidopsis ABPs, MAPs, and IF proteins are represented by individual genes and most were represented as as small gene families. However, several classes of cytoskeletal genes including myosin, eEF1α, CLIP, tea1, and kinesin are part of large gene families with 20 to 70 potential gene members each. This treasure trove of data provides an unprecedented opportunity to make rapid advances in understanding the complex plant cytoskeletal proteome. However, the functional analysis of these proposed cytoskeletal proteins and their mutants will require detailed analysis at the cell biological, molecular genetic, and biochemical levels. New approaches will be needed to move more efficiently and rapidly from this mass of DNA sequence to functional studies on cytoskeletal proteins.

Ultrasensitive behavior in the synthesis of storage polysaccharides in cyanobacteria

The glycogen synthetic pathway operates ultrasensitively as a function of the ADPglucose pyrophosphorylase (ADPGlcPPase) allosteric effectors, 3-phosphoglycerate and Pi, in permeabilized cells of the cyanobacterium Anabaena PCC 7120. In vitro data previously showed that the ultrasensitive behavior of ADPGlcPPase depends upon cross-talk between the two allosteric effectors, the enzyme's response being additionally modulated by molecular crowding [D.F. Gómez Casatiet al. (2000) Biochem J 350:139-147]. In the present work we show, experimentally and with a mathematical model, that alpha-1,4-glucan synthesis is also ultrasensitive in cells due to the propagation of the switch-like behavior of ADPGlcPPase to the synthetic pathway. Amplifications of up to 20-fold in storage-polysaccharide synthesis can be achieved with a modest 6.7-fold increase in 3-phosphoglycerate in the presence of 5 mM Pi in contrast to the 30-fold necessary in its absence. This is the first time that this phenomenon has been reported to occur in the glycogen synthetic pathway of a photosynthetic prokaryote. The implications of the results for plant cell physiology during light-dark transitions are discussed.

Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray

The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3' ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.

Coherent and robust modulation of a metabolic network by cytoskeletal organization and dynamics

In order to investigate the influence of cytoskeletal organization and dynamics on cellular biochemistry, a mathematical model was formulated based on our own experimental evidence. The model couples microtubular protein (MTP) dynamics to the glycolytic pathway and its branches: the Krebs cycle, ethanolic fermentation, and the pentose phosphate (PP) pathway. Results show that the flux through glycolysis coherently and coordinately increases or decreases with increased or decreased levels of polymerized MTP, respectively. The rates of individual enzymatic steps and metabolite concentrations change with the polymeric status of MTP throughout the metabolic network. Negative control is exerted by the PP pathway on the glycolytic flux, and the extent of inhibition depends inversely on the polymerization state of MTP, i.e. a high degree of polymerization relieves the negative control. The stability of the model's steady state dynamics for a wide range of variation of metabolic parameters increased with the degree of polymerized MTP. The findings indicate that the organization of the cytoskeleton bestows coherence and robustness to the coordination of cellular metabolism.

Identification of genes expressed in response to light stress in leaves of Arabidopsis thaliana using RNA differential display

The plant cell responds to light stress by the expression of genes encoding specific stress proteins with possible protective functions. Five genes, the mRNA levels of which increased drastically in response to light stress in mature green leaves of Arabidopsis thaliana were identified and isolated by the differential display technique. These genes were designated Lsr1-Lsr5 (light stress-regulated). Northern blot analysis demonstrated that the transcript level of Lsr1-Lsr5 increased 4- to 17-fold under light stress conditions as compared with leaves incubated at low intensity light. Further analysis of the Lsr1-Lsr5 transcript level under cold stress, heat shock, wounding, desiccation, salt stress, oxidative stress and UV-A irradiation showed that the expression of all five genes was triggered by more than one stress factor. Thus, it was expected that isolated genes encode proteins involved in general stress responses. Homology searches revealed that all of the isolated cDNAs were represented in the GenBank in genomic DNAs and expressed sequence tag (EST) cDNA clones. The Lsr1-Lsr4 genes encoded cytoplasmic proteins with assigned identities, such as ERD15 (early responsive to dehydration), ACT2 (actin 2), LEA14 (late embryogenesis abundant) and MT1a (metallothionein class 1a), respectively. Light stress had not yet been reported to induce or enhance the expression of these genes. The Lsr5 clone encoded a novel protein with high similarity to beta-1,3-galactosyltransferases from human and primates predicted to be located in the Golgi body. Three ORFs homologous to the Lsr5 gene were found on chromosome I and IV of Arabidopsis indicating that a multigene family of these proteins exists in plants. The possible role of Lsr gene products in light stress defences is discussed.

Measurement of the glycogen synthetic pathway in permeabilized cells of cyanobacteria

A simple, rapid and reliable procedure for permeabilizing cyanobacterial cells and measuring the glycogen synthetic pathway in situ, is presented. Cells from Anabaena sp. strain PCC 7120 were permeabilized with a mixture of toluene:ethanol (1:4 v/v). Fluorescence microscopy of cells incubated with fluorescein diacetate showed Anabaena non-permeabilized cells as green fluorescents, whereas permeabilized (viable) cells exhibited the intrinsic red fluorescence. Labelled alpha-1,4-glucan was recovered when permeabilized cells were incubated with the substrates of ADP-glucose pyrophosphorylase or glycogen synthase. The kinetic and regulatory properties of both enzymes could be reproduced in situ. The simplicity of the procedure and the ability to measure in situ glucan fluxes show the methodology as useful for studying the intracellular regulation of storage polysaccharides in a photosynthetic prokaryote.

Regulation of a wheat actin-depolymerizing factor during cold acclimation

We have previously shown that the wheat (Triticum aestivum) TaADF gene expression level is correlated with the plants capacity to tolerate freezing. Sequence analysis revealed that this gene encodes a protein homologous to members of the actin-depolymerizing factor (ADF)/cofilin family. We report here on the characterization of the recombinant TaADF protein. Assays for ADF activity showed that TaADF is capable of sequestering actin, preventing nucleotide exchange, and inducing actin depolymerization. In vitro phosphorylation studies showed that TaADF is a substrate for a wheat 52-kD kinase. The activity of this kinase is modulated by low temperature during the acclimation period. Western-blot analyses revealed that TaADF is expressed only in cold-acclimated Gramineae species and that the accumulation level is much higher in the freezing-tolerant wheat cultivars compared with the less tolerant ones. This accumulation was found to be regulated by a factor(s) encoded by a gene(s) located on chromosome 5A, the chromosome most often found to be associated with cold hardiness. The induction of an active ADF during cold acclimation and the correlation with an increased freezing tolerance suggest that the protein may be required for the cytoskeletal rearrangements that may occur upon low temperature exposure. These remodelings might be important for the enhancement of freezing tolerance.

Kinetic and structural analysis of the ultrasensitive behaviour of cyanobacterial ADP-glucose pyrophosphorylase

The kinetic and (supra)molecular properties of the ultrasensitive behaviour of ADP-glucose pyrophosphorylase (AGPase) from Anabaena PCC 7120 (a cyanobacterium) were exhaustively studied. The response of the enzyme toward the allosteric activator 3-phosphoglycerate (3PGA) occurs with ultrasensitivity as a consequence of the cross-talk with the inhibitor P(i). Molecular 'crowding' renders AGPase more sensitive to the interplay between the allosteric regulators and, consequently, enhances the ultrasensitive response. In crowded media, and when orthophosphate is present, the activation kinetics of the enzyme with 3PGA proceed with increased co-operativity and reduced affinity toward the activator. Under conditions of ultrasensitivity, the enzyme's maximal activation takes place in a narrow range of 3PGA concentrations. Moreover, saturation kinetics of the enzyme with respect to its substrates, glucose 1-phosphate and ATP, were different at low or high 3PGA levels in crowded media. Only under the latter conditions did AGPase exhibit discrimination between low or high levels of the activator, which increased the affinity toward the substrates and the maximal activity reached by the enzyme. Studies of fluorescence emission of tryptophan residues, fourth-derivative spectroscopy and size-exclusion chromatography indicated that the ultrasensitive behaviour is correlated with intramolecular conformational changes induced in the tertiary structure of the homotetrameric enzyme. The results suggest a physiological relevance of the ultrasensitive response of AGPase in vivo, since the enzyme could be subtly sensing changes in the levels of allosteric regulators and substrates, and thus determining the flux of metabolites toward synthesis of storage polysaccharides.